Clinical characterization and genetic analysis of two Chinese pedigrees affected with Familial adenomatous polyposis caused by variants of MUTYH gene

ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG)

DNA-based screening and population health: a points to consider statement for programs and sponsoring organizations from the American College of Medical Genetics and Genomics (ACMG)

Updated recommendations for CFTR carrier screening: A position statement of the American College of Medical Genetics and Genomics (ACMG)

The tricky matter of secondary genomic findings

PurposeComparison of variant frequencies in the general population has become an essential part of the American College of Medical Genetics and Genomics (ACMG) standards and guidelines for interpreting sequence variants. We determined the optimal number of relevant ethnic controls that should be used to accurately calculate the odds ratio (OR) of genetic variants.Materials and MethodsUsing the ACMG guidelines, we reclassified BRCA1 and BRCA2 mutations and variants of unknown significance in 745 Korean patients susceptible to hereditary breast and ovarian cancer compared with 1,314 Korean population controls.ResultsWe observed that the ORs were falsely inflated when we analyzed several variants using non-Korean population data. Our simulation indicated that the number of controls needed for the lower limit of a 95% confidence interval to exceed 1.0 varied according to the frequency of the variant in each patient group, with more than 820 controls needed for a variant existing in 1% of cases. Using a sufficient number of relevant population data, we could efficiently classify variants and identified the BRCA1 p.Leu1780Pro mutation as a possible pathogenic founder mutation in Korean patients.ConclusionOur study suggests that BRCA1 p.Leu1780Pro is a novel pathogenic mutation found in Korean patients. We also determined the optimal number of relevant ethnic controls needed for accurate variant classification according to the ACMG guidelines.

To analyze the clinical phenotype and genetic etiology of a child with Multiple congenital anomalies-hypotonia-seizures syndrome 1 (MCAHS1). Clinical data of a 2-year-old boy who had presented at the Affiliated Hospital of Qingdao University in March 2023 for "intermittent limb twitching for 2 years" was collected. Peripheral blood samples were collected from the child and his parents for whole-exome sequencing (WES). Candidate variants were verified by Sanger sequencing and bioinformatic analysis based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). The child had manifested with distinctive facial features, limb deformities, hypotonia, motor and intellectual delays, and epileptic seizures. WES revealed that he has harbored compound heterozygous variants of the PIGN gene, namely c.963G>A (p.Q321=) and c.994A>T (p.I332F), which were inherited from his phenotypically normal mother and father, respectively. Based on the ACMG guidelines, the c.963G>A was classified as a pathogenic variant (PVS1+PM2_Supporting+PM3), whilst the c.994A>T was classified as a variant of uncertain significance (PM2_Supporting+PP3). Above discovery has expanded the mutational spectrum of the PIGN gene variants associated with MCAHS1, which may facilitate delineation of its genotype-phenotype correlation.

To explore the clinical characteristics and variant of FBP1 gene in a child with Fructose-1,6-bisphosphatase deficiency (FBP1D), and review the literature on the clinical characteristics and gene mutations of FBP1D in the Chinese population. A FBP1D proband due to variant of FBP1 gene who was admitted to Women and Children's Hospital of Ningbo University on August 10, 2021 due to "vomiting for 1 day" was selected as the study subject. Clinical data of the child were retrospectively collected. Whole exome sequencing (WES) was performed on the child, and candidate variants identified in the child were validated by Sanger sequencing in both the child and his parents. The difference between wild type and variant FBP1 protein were compared using AlphaFold v3.0.1 and PyMOL v2.5.6. The pathogenicity of candidate variant was rated according to the Standards and Guidelines for the Interpretation of Sequence Variants released by American College of Medical Genetics and Genomics (ACMG) (hereinafter referred to as ACMG guidelines). Using keywords such as "FBP1 gene" and "fructose-1,6-bisphosphatase deficiency" both in Chinese and English, relevant literature on FBP1D patients caused by FBP1 gene variants in the Chinese population were retrieved from the PubMed database, CNKI, and Wanfang Data Knowledge Service Platform, and the genetic variant and clinical phenotypes of FBP1D patients reported in the literature were analyzed. The literature retrieval time was set from the establishment of each database to October 31st, 2024. This study was approved by the Women and Children's Hospital of Ningbo University (Ethics No.: 2020-048). The proband was presented with repeated infections, nausea, vomiting, and mental illness. The auxiliary examination revealed hypoglycemia, acidosis, liver and kidney dysfunction, hyperlipidemia and hepatomegaly. WES and Sanger sequencing revealed that the child has harbored compound heterozygous variants of the FBP1 gene, including a de novo nonsense variant c.778G>T (p.G260*) in exon 6 and a maternally derived missense variant c.923C>G (p.P308R) in exon 7. The c.923C>G was known as a likely pathogenic variant, while c.778G>T has not been included in the databases such as HGMD, ClinVar, 1000 Genomes, ExAC, dbSNP, and gnomAD. Protein structure prediction shows that the c.778G>T (p.G260*) variant may result in a premature termination codon, resulting in loss of a β-fold in a core region, which may significantly reduce the stability of its protein product and affect its function. Based on the ACMG guidelines, the c.778G>T (p.G260*) variant was rated as likely pathogenic (PVS1_Strong+PM2_Supporting+PP4+PM6). Literature review has identified 32 patients from 23 Chinese families with FBP1D due to FBP1 gene variants. Together with the case reported in this study, in total 33 patients were analyzed. Among them, 22 cases were males (66.7%) with hypoglycemia, metabolic acidosis, vomiting, seizures, hyperlactatemia, and ketosis as the primary clinical phenotypes. After treatment, only 1 case (3.0%) died due to cerebral hernia, while the remaining 32 (97.0%) had favorable outcomes. Four cases (12.1%) exhibited developmental delay. A total of 66 FBP1 gene variant sites were identified, which involved 22 variant types, predominantly missense mutations (31 gene variant sites). These variants were mainly located in exon 7 of the gene (25 variant sites), with c.490G>A (16.7%, 11/66), c.960_961insG (19.7%, 13/66), c.355G>A (12.1%, 8/66), and c.704delC (9.1%, 6/66) being the most common variants. The heterozygous variant of the FBP1 gene probably underlay the FBP1D in this child. Above finding has enriched the phenotypic and mutational spectrum of the FBP1 gene and provided a basis for genetic counseling and clinical decision-making.

The uncertainty of copy number variants: pregnancy decisions and clinical follow-up

Background: Whole-exome-sequencing (WES) is becoming a common molecular diagnostic test for patients with genetic disorders. However, this technique allows the identification not only of mutations responsible for the disease under investigation, but also of variants potentially causing other diseases, the so called “incidental findings” (IFs). The American College of Medical Genetics and Genomics (ACMG) stated that IFs should be reported based on clinical validity and utility and indicated a list of 56 actionable genes. Among these, nearly half (20/56) are major genes associated with channelopathies and cardiomyopathies. Despite these recommendations, most of the studies so far published, reported also mutations in minor genes among the actionable findings. Methods: WES was performed in 5891 individuals without known channelopathies or cardiomyopathies. Exome data were first filtered based on genotype quality. Subsequently, a frequency filter was applied, considering 1000 Genomes, ExAC and our internal exome database. Variants reported as pathogenic in ClinVar or novel but expected to be pathogenic (nonsense, frameshift and splice) were further investigated, following the ACMG guidelines. Major (20) and minor (73) genes associated with channelopathies and cardiomyopathies were evaluated. Results: We identified 3514 variants in the 93 genes under investigation, after applying the quality and frequency filters. Eight variants were classified as pathogenic and 52 as likely pathogenic and they were detected in around 1% of the individuals. The vast majority (85%) of pathogenic or likely pathogenic variants were located in the 20 actionable genes indicated by ACMG. The inclusion of minor genes increased the number of variants of unknown significance (VUS), from 865 to 3454. Conclusion: Our data support the ACMG recommendations in reporting only IFs identified in the 20 major cardiac actionable genes. Indeed, the inclusion of minor genes is mainly increasing the number of VUS, without significantly impacting the number of pathogenic and likely pathogenic variants. The percentage of individuals with potentially clinical relevant variants in these genes is too high in relation to the disease-prevalence: a cardiologic evaluation is warranted.

Disclosure: L. Grater: None. Z. Hawkins: None. L.C. Layman: None.Introduction: Idiopathic hypogonadotropic hypogonadism (IHH) is a disorder characterized by a deficiency in gonadotropin-releasing hormone (GnRH) neuron migration, or GnRH production or action, leading to delayed or absent sexual development and subsequent infertility. Subtypes of IHH include hyposmic/anosmic (Kallmann syndrome), and normosmic forms. To date, variants in more than 50 genes have been reported as causal in IHH/KS, but not all variants have been confirmed to impair function, potentially overestimating pathogenic variants. We hypothesized that true causative variants as classified by the American College of Medical Genetics and Genomics (ACMG) published guidelines are less common than what are reported. Methods: We reviewed 49 publications reporting 306 IHH/KS-related genetic variants which were considered causal. Each specific variant was entered into VarSome and ClinVar, two search engines that apply the most current ACMG classification: Pathogenic (P), Likely Pathogenic (LP), Variants of Uncertain Significance (VUS), Likely Benign (LB), or Benign (B). Results: 306 variants from 49 studies were described as loss of function, pathogenic, likely pathogenic, disease-causing, deleterious, or damaging, with all terms collectively regarded as indicating pathogenicity. However, using VarSome, 146/306 (47.7%) of purported “causative” variants were classified as either P or LP—78 (25.5%) was deemed as P and 68 (22.2%) as LP. Additionally, 83/306 (27.10%) were classified as VUS and 77/306 (25.2%) were classified as LB or B. ClinVar reported 87/306 (28.4%) as P/LP, 41/306 (13.4%) as VUS, 19/306 (6.2%) as LB/B, 38/306 (12.4%) as “conflicting,” and 121/360 (39.5%) as “no data.” Among the 146 variants classified as LP/P by VarSome, 13.7% were frameshift, 66.4% missense, 17.1% nonsense, and 2.7% noncoding. In contrast, 92.8% of the 83 variants classified as VUS by VarSome were missense, 2.4% nonsense, and 4.8% were in-frame deletions. Conclusions: Just under half of the putative variants were called as P/LP by Varsome, whereas one-fourth were VUS and one-fourth were B/LB. ClinVar only called <30% of these as P/LP. These findings highlight more stringent classification criteria of VarSome and ClinVar, further emphasizing the need for standardized variant classification, based on ACMG guidelines. Supportive evidence for a P/LP variant comes from in silico prediction, low frequency of alleles in the gnomAD database, impaired function in vitro, and segregation with the phenotype in several or numerous families. Failure to meet these benchmarks leads to misclassification, which may affect clinical interpretation and patient care.Presentation: Sunday, July 13, 2025

e22528 Background: The familiar history is indispensable to clinical investigation during genetic counseling and the new molecular techniques allowed the identification of hereditary cancer predisposition syndromes (CPS). However, the classification systems of these syndromes are difficulty and very complex. In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for the assessment of variants in genes associated with Mendelian diseases to reduce the subjectivity bias of mutation variants classified as risk. Methods: To show the difficulty of classification of these variants we describe a case report of a family from countryside of Brazil in which there is a high rate of inbreeding. This family has three brothers with polyposis and colorectal cancer between 51 and 60 years-old. Results: The index-case had multiple polyps, developed colorectal cancer at 51 years-old and had a familiar history of two brother dead by colorectal cancer after polyposis and nine brother without familiar history of cancer, a father dead at 38 years-old by non-specific lung-disease and a mother alive at 83 years-old. There was no description of other cases of cancer among uncles and grandparents. The index-case performe a NSG genetic painel to CPS and showed a homozygosis variant in MUTYH gene: NM_001048174.1: c.253T &gt; C:p.(Trp85Arg), that was classified as variant of uncertain significance (VUS). MUTYH is a base excision repair enzyme, it plays a crucial role in the correction of DNA errors and may be considered a cell protective factor and is associated with MUTYH-related polyposis (MAP). MAP is an autosomal recessive CPS and presents a phenotype that overlaps attenuated polyposis and familial adenomatous polyposis, increasing the risk of colorectal cancer in 43-63% up to 60 years or 80% if there is no surveillance/tracking. In view of the family history that suggests autosomal recessive inheritance, with a homozygous variant absent in the database of population controls (gnomAD) and in which in silico predictors indicate the effect of this variant as deleterious, the management of this family must be carried out considering it as a potential high-risk pathogenic variant. Conclusions: While the classification criteria for the variants are being refined, we reinforce the importance of a careful family history in the approach to CPS in order to offer an appropriate clinal conduct in the prevention of hereditary cancer.

Missense variants in the MYH7-encoded MYH7 (beta myosin heavy chain 7) represent a leading cause of hypertrophic cardiomyopathy (HCM). MYH7-specific American College of Medical Genetics and Genomics (ACMG) variant classification guidelines were released recently but have yet to be assessed independently. We set out to assess the performance of the MYH7-specific ACMG guidelines and determine if the addition of phenotype-enhanced criteria (PE-ACMG) using the HCM Genotype Predictor Score can further reduce the burden of variants of uncertain significance (VUS). Re-assessment was performed on 70 MYH7-variants in 121 unique patients from Mayo Clinic, and an independent cohort of 54 variants in 70 patients from Royal Prince Alfred Hospital (Australia). Qualifying variants were re-adjudicated using both standard ACMG and MYH7-ACMG guidelines, and HCM Genotype Predictor Score was used to provide a validated measure of strength of clinical phenotype to be incorporated into the MYH7-ACMG framework. Among Mayo Clinic identified variants, 11/70 (16%) were classified as pathogenic (P), 10/70 (14%) as likely pathogenic, and 49/70 (70%) as a VUS. A similar distribution was seen in the Australian patients (12/54 [22%] P, 12/54 [22%] likely pathogenic, and 30/54 [56%] VUS; P=not significant). Application of the MYH7-ACMG resulted in a nonsignificant reduction of the VUS burden in both cohorts from 49/70 to 39/70 (56%; P=0.1; Mayo Clinic) and from 30/54 to 20/54 (37%; P=0.1; Australia). Using the combined PE-MYH7-ACMG framework, the VUS decreased significantly from 49 to 27 (P<0.001, Mayo Clinic) and from 30 to 16 (P<0.001; Australia). Use of the MYH7-specific guidelines alone failed to significantly decrease VUS burden in 2 independent cohorts. However, a significant reduction in VUS burden was observed after the addition of phenotypic criteria. Using a patient's strength of sarcomeric HCM phenotype for variant adjudication can increase significantly the clinical utility of genetic testing for patients with HCM.

To explore the clinical phenotype and genetic characteristics of a patient with Progressive pseudorheumatoid dysplasia (PPRD) due to compound heterozygous variants of CCN6 gene. A patient who was admitted to Qilu Hospital of Shandong University due to "bilateral finger joint deformity, bilateral hip and knee joint movement limitation for 19 years" was selected as the study subject. Clinical data of the patient were retrospectively collected. Peripheral blood samples were collected from the patient and her parents and subjected to whole exome sequencing (WES). Long-read sequencing (LRS) and Sanger sequencing were used to verify the candidate variants. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the pathogenicity of candidate variants was classified. This study was approved by the Medical Ethics Committee of Qilu Hospital of Shandong University (Ethics No.: KYLL-202502 061). The patient, a 23-year-old female, presented with progressive polyarticular deformity, limited movement and abnormal growth and development since childhood. She was initially misdiagnosed as Ankylosing spondylitis and had poor response to sulphasalazine and etoricoxib treatment. WES revealed that she has harbored two heterozygous variants of the CCN6 gene (NM_198239.2), namely c.348C>A and c.676G>C. LRS confirmed that the two variants are located on two homologous chromosomes and constitute compound heterozygous variants. Based on the ACMG guidelines, both variants were rated as pathogenic (PVS1+PM2_Supporting+PM3; PM1+PM2_Supporting+PM3_Supporting+PM5+PP3_Strong). The c.676G>C variant has not been recorded by the HGMD and ClinVar databases. The c.348C>A and c.676G>C compound heterozygous variants of the CCN6 gene probably underlay the pathogenesis of PPRD in this patient. Above finding has enriched the mutational spectrum of PPRD and provided a basis for the clinical diagnosis and genetic counseling.

Guidelines support the return of incidental genomic findings

BackgroundThe American College of Medical Genetics and Genomics (ACMG)-recommended five variant classification categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign) have been widely used in medical genetics. However, these guidelines are fundamentally constrained in practice owing to their focus upon Mendelian disease genes and their dichotomous classification of variants as being either causal or not. Herein, we attempt to expand the ACMG guidelines into a general variant classification framework that takes into account not only the continuum of clinical phenotypes, but also the continuum of the variants’ genetic effects, and the different pathological roles of the implicated genes.Main bodyAs a disease model, we employed chronic pancreatitis (CP), which manifests clinically as a spectrum from monogenic to multifactorial. Bearing in mind that any general conceptual proposal should be based upon sound data, we focused our analysis on the four most extensively studied CP genes, PRSS1, CFTR, SPINK1 and CTRC. Based upon several cross-gene and cross-variant comparisons, we first assigned the different genes to two distinct categories in terms of disease causation: CP-causing (PRSS1 and SPINK1) and CP-predisposing (CFTR and CTRC). We then employed two new classificatory categories, “predisposing” and “likely predisposing”, to replace ACMG’s “pathogenic” and “likely pathogenic” categories in the context of CP-predisposing genes, thereby classifying all pathologically relevant variants in these genes as “predisposing”. In the case of CP-causing genes, the two new classificatory categories served to extend the five ACMG categories whilst two thresholds (allele frequency and functional) were introduced to discriminate “pathogenic” from “predisposing” variants.ConclusionEmploying CP as a disease model, we expand ACMG guidelines into a five-category classification system (predisposing, likely predisposing, uncertain significance, likely benign, and benign) and a seven-category classification system (pathogenic, likely pathogenic, predisposing, likely predisposing, uncertain significance, likely benign, and benign) in the context of disease-predisposing and disease-causing genes, respectively. Taken together, the two systems constitute a general variant classification framework that, in principle, should span the entire spectrum of variants in any disease-related gene. The maximal compliance of our five-category and seven-category classification systems with the ACMG guidelines ought to facilitate their practical application.