ClinVar Miner

Submissions for variant NM_021922.3(FANCE):c.1610G>T (p.Ter537Leu)

gnomAD frequency: 0.00020  dbSNP: rs139547269
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000648999 SCV000770820 uncertain significance Fanconi anemia complementation group E 2022-09-07 criteria provided, single submitter clinical testing This sequence change disrupts the translational stop signal of the FANCE mRNA. It is expected to extend the length of the FANCE protein by 27 additional amino acid residues. This variant is present in population databases (rs139547269, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with FANCE-related conditions. ClinVar contains an entry for this variant (Variation ID: 539293). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Baylor Genetics RCV000648999 SCV001482801 uncertain significance Fanconi anemia complementation group E 2020-03-10 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002235507 SCV002511864 uncertain significance not specified 2022-04-20 criteria provided, single submitter clinical testing Variant summary: FANCE c.1610G>T (p.X537LeuextX27) changes the termination codon and is predicted to lead to an extended protein with additional amino acids added to the normal C-terminus. FANCE c.1610G>T (p.X537LeuextX27) causes a frameshift which results in an extension of the protein. The variant allele was found at a frequency of 4.8e-05 in 251474 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in FANCE causing Fanconi Anemia (4.8e-05 vs 0.00048), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1610G>T in individuals affected with Fanconi Anemia and no experimental evidence demonstrating its impact on protein function have been reported. Two 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 uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
Sema4, Sema4 RCV002257904 SCV002527951 likely pathogenic Fanconi anemia 2021-06-22 criteria provided, single submitter curation

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