ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.3181A>G (p.Ser1061Gly)

gnomAD frequency: 0.00002  dbSNP: rs369878171
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000458688 SCV000547761 uncertain significance Fanconi anemia 2024-01-09 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 1061 of the FANCA protein (p.Ser1061Gly). This variant is present in population databases (rs369878171, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with FANCA-related conditions. ClinVar contains an entry for this variant (Variation ID: 408187). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt FANCA protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV000765326 SCV000896586 uncertain significance Fanconi anemia complementation group A 2024-02-06 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV001821266 SCV002070648 uncertain significance not specified 2019-04-26 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000458688 SCV002534990 uncertain significance Fanconi anemia 2021-09-07 criteria provided, single submitter curation
Quest Diagnostics Nichols Institute San Juan Capistrano RCV003477952 SCV004218549 uncertain significance not provided 2022-08-25 criteria provided, single submitter clinical testing The frequency of this variant in the general population, 0.000008 (2/251340 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in patients with adenocarcinoma and small cell lung cancer (PMID: 32107087 (2020)). Additionally, the variant was reported to co-occur with two other pathogenic FANCA variants, in a patient with refractory leukocytopenia and thrombocytopenia (PMID: 31030435 (2019)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.
Natera, Inc. RCV000765326 SCV001462886 uncertain significance Fanconi anemia complementation group A 2020-09-16 no assertion criteria provided clinical testing

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