ClinVar Miner

Submissions for variant NM_004629.2(FANCG):c.1761-2A>C

gnomAD frequency: 0.00001  dbSNP: rs765150956
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV001781088 SCV002017716 likely pathogenic Fanconi anemia complementation group G 2020-11-13 criteria provided, single submitter clinical testing
Lifecell International Pvt. Ltd RCV001781088 SCV003920842 likely pathogenic Fanconi anemia complementation group G criteria provided, single submitter clinical testing A Homozygote, Splice site acceptor variant c.1761-2A>C in Exon 13 of the FANCG gene that results in the amino acid substitution was identified. The observed variant has a minor allele frequency of 0.0001% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and the REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. The variant has been reported to ClinVar as Likely pathogenic with a status of (0 stars) no assertion criteria provided (Variation ID 1324383 as of 2021-11-29). Mutations in the FANCG gene have been well documented in cases of Fanconi anemia (de Winter, J P et al., 1998). Based on the above evidence this variant has been classified as Likely pathogenic according to the ACMG guidelines.
Neuberg Centre For Genomic Medicine, NCGM RCV001781088 SCV004101539 likely pathogenic Fanconi anemia complementation group G criteria provided, single submitter clinical testing The splice site variant c.1761-2A>C in FANCG gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has been reported to the ClinVar database as Likely Pathogenic. The c.1761-2A>C variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.0008% is reported in gnomAD. The variant affects an invariant splice nucleotide and is expected to cause loss of function. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

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