ClinVar Miner

Submissions for variant NM_001018115.3(FANCD2):c.696-121C>G

dbSNP: rs2086862509
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004526811 SCV005039257 likely pathogenic Fanconi anemia 2024-03-21 criteria provided, single submitter clinical testing Variant summary: FANCD2 c.696-121C>G is located at a position not widely known to affect splicing. Several computational tools predict a significant impact on normal splicing: Three predict the variant strengthens a cryptic 5' donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing. The variant allele was found at a frequency of 3.5e-05 in 591794 control chromosomes, predominantly at a frequency of 0.00034 within the South Asian subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for a pathogenic variant in FANCD2 causing Fanconi Anemia (3.5e-05 vs 0.00048), allowing no conclusion about variant significance. c.696-121C>G has been reported in the literature in individuals affected with Fanconi Anemia. These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% of normal activity. ClinVar contains an entry for this variant (Variation ID: 929644). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Leiden Open Variation Database RCV001194904 SCV001364766 pathogenic Fanconi anemia complementation group D2 2020-02-28 no assertion criteria provided curation Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.

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