ClinVar Miner

Submissions for variant NM_001113378.2(FANCI):c.3493del (p.Asp1165fs)

dbSNP: rs758597713
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000457201 SCV000547775 pathogenic Fanconi anemia 2023-12-05 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Asp1165Thrfs*34) in the FANCI gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCI are known to be pathogenic (PMID: 17452773, 17460694). This variant is present in population databases (rs758597713, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with head and neck squamous cell carcinoma (PMID: 28678401). ClinVar contains an entry for this variant (Variation ID: 408200). For these reasons, this variant has been classified as Pathogenic.
AiLife Diagnostics, AiLife Diagnostics RCV002223210 SCV002501463 pathogenic not provided 2021-06-11 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000457201 SCV002529840 likely pathogenic Fanconi anemia 2021-01-23 criteria provided, single submitter curation
Fulgent Genetics, Fulgent Genetics RCV001194983 SCV002811465 pathogenic Fanconi anemia complementation group I 2021-07-23 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000457201 SCV002819343 likely pathogenic Fanconi anemia 2022-12-08 criteria provided, single submitter clinical testing Variant summary: FANCI c.3493delG (p.Asp1165ThrfsX34) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been associated with Fanconi Anemia in HGMD. The variant allele was found at a frequency of 5.2e-05 in 251486 control chromosomes. c.3493delG has been reported in the literature as a compound heterozygous genotype in individuals affected with Fanconi Anemia (Chandrasekharappa_2017). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three 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 pathogenic (n=2) and likely pathogenic (n=1) . Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV001194983 SCV004197156 pathogenic Fanconi anemia complementation group I 2023-10-15 criteria provided, single submitter clinical testing
Leiden Open Variation Database RCV001194983 SCV001364857 pathogenic Fanconi anemia complementation group I 2013-10-04 no assertion criteria provided curation Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

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