ClinVar Miner

Submissions for variant NM_000136.3(FANCC):c.1534-5del

dbSNP: rs748342368
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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 RCV000458841 SCV000560619 likely benign Fanconi anemia 2024-11-26 criteria provided, single submitter clinical testing
GeneDx RCV002461222 SCV000728006 likely benign not provided 2024-02-24 criteria provided, single submitter clinical testing See Variant Classification Assertion Criteria.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000610407 SCV001363460 uncertain significance not specified 2019-10-10 criteria provided, single submitter clinical testing Variant summary: FANCC c.1534-5delT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 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 4.8e-05 in 250192 control chromosomes, predominantly at a frequency of 0.00035 within the Latino subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in FANCC causing Fanconi Anemia Group C (0.00035 vs 0.0018), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1534-5delT in individuals affected with Fanconi Anemia Group C and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submissions (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV002461222 SCV004218670 uncertain significance not provided 2022-12-24 criteria provided, single submitter clinical testing To the best of our knowledge, the variant has not been reported in the published literature. The frequency of this variant in the general population, 0.00037 (13/35416 chromosomes in Latino/Admixed American subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on FANCC mRNA splicing yielded inconclusive findings. Based on the available information, we are unable to determine the clinical significance of this variant.
Fulgent Genetics, Fulgent Genetics RCV001271439 SCV005677779 likely benign Fanconi anemia complementation group C 2024-06-21 criteria provided, single submitter clinical testing
Natera, Inc. RCV001271439 SCV001452570 likely benign Fanconi anemia complementation group C 2020-09-16 no assertion criteria provided clinical testing

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