ClinVar Miner

Submissions for variant NM_000136.3(FANCC):c.840G>A (p.Ser280=)

gnomAD frequency: 0.00154  dbSNP: rs34671520
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124966 SCV000168406 benign not specified 2014-01-09 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 RCV000205819 SCV000260824 benign Fanconi anemia 2021-12-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV000565157 SCV000673299 likely benign Hereditary cancer-predisposing syndrome 2016-11-17 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000124966 SCV000919325 benign not specified 2018-11-30 criteria provided, single submitter clinical testing Variant summary: FANCC c.840G>A alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00056 in 277166 control chromosomes, predominantly at a frequency of 0.0045 within the African subpopulation in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 2.55 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.840G>A in individuals affected with Fanconi Anemia Group C and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Genetic Services Laboratory,University of Chicago RCV000124966 SCV002070770 likely benign not specified 2019-06-11 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000205819 SCV002535126 likely benign Fanconi anemia 2021-02-04 criteria provided, single submitter curation
Natera, Inc. RCV000205819 SCV002081213 likely benign Fanconi anemia 2017-05-10 no assertion criteria provided clinical testing

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