ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.2667del (p.Ser890fs) (rs1555545517)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665563 SCV000789708 likely pathogenic Fanconi anemia, complementation group A 2017-02-15 criteria provided, single submitter clinical testing
GeneDx RCV001008375 SCV001168143 likely pathogenic not provided 2018-09-21 criteria provided, single submitter clinical testing The c.2667delC variant in the FANCA gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.2667delC variant causes a frameshift starting with codon Serine 890, changes this amino acid to an Alanine residue, and creates a premature Stop codon at position 31 of the new reading frame, denoted p.Ser890AlafsX31. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.2667delC variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.2667delC as a likely pathogenic variant.
Invitae RCV001382564 SCV001581404 pathogenic Fanconi anemia 2020-02-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser890Alafs*31) in the FANCA gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with FANCA-related conditions. ClinVar contains an entry for this variant (Variation ID: 550737). Loss-of-function variants in FANCA are known to be pathogenic (PMID: 19367192). For these reasons, this variant has been classified as Pathogenic.

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