ClinVar Miner

Submissions for variant NM_031471.6(FERMT3):c.1080-5C>T

gnomAD frequency: 0.00020  dbSNP: rs143722885
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001445354 SCV001648382 likely benign Leukocyte adhesion deficiency 3 2023-08-10 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002509683 SCV002819301 uncertain significance not specified 2022-12-06 criteria provided, single submitter clinical testing Variant summary: FERMT3 c.1080-5C>T in transcript NM_031471 alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00014 in 250942 control chromosomes. To our knowledge, no occurrence of c.1080-5C>T in individuals affected with Leukocyte Adhesion Deficiency, Type III and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as likely benign. While the variant is predicted to result in a nonsense mutation in another transcript (p.R363*, NM_178443/ENST00000279227), this transcript is expressed at low levels in whole blood and all other tissues reported in the GTEx Transcript Browser, compared to NM_031471/ENST00000345728 which has the highest levels of expression. Based on the evidence outlined above, the variant was classified as uncertain significance.

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