ClinVar Miner

Submissions for variant NM_000136.3(FANCC):c.1156T>C (p.Ser386Pro)

gnomAD frequency: 0.00236  dbSNP: rs41281202
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000120969 SCV000211068 benign not specified 2014-08-15 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001082314 SCV000253074 benign Fanconi anemia 2024-01-31 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000224016 SCV000281484 uncertain significance not provided 2015-06-04 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
Ambry Genetics RCV000566496 SCV000673296 likely benign Hereditary cancer-predisposing syndrome 2019-03-25 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Mendelics RCV000709083 SCV000838345 likely benign Fanconi anemia complementation group C 2018-07-02 criteria provided, single submitter clinical testing
Mendelics RCV000988205 SCV001137842 likely benign Fanconi anemia complementation group A 2019-05-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000120969 SCV001363458 likely benign not specified 2019-02-01 criteria provided, single submitter clinical testing Variant summary: FANCC c.1156T>C (p.Ser386Pro) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00074 in 277128 control chromosomes, predominantly at a frequency of 0.0079 within the African subpopulation in the gnomAD database, including 1 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 4.5 fold of the estimated maximal expected allele frequency for a pathogenic variant in FANCC causing Fanconi Anemia Group C phenotype (0.0018), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.1156T>C in individuals affected with Fanconi Anemia Group C and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign (3x) and once as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.
Baylor Genetics RCV000709083 SCV001525765 uncertain significance Fanconi anemia complementation group C 2018-07-16 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000224016 SCV002046913 benign not provided 2021-04-29 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000120969 SCV002066055 likely benign not specified 2021-08-27 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV001082314 SCV002535082 likely benign Fanconi anemia 2021-02-25 criteria provided, single submitter curation
ITMI RCV000120969 SCV000085137 not provided not specified 2013-09-19 no assertion provided reference population

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