ClinVar Miner

Submissions for variant NM_001369369.1(FOXN1):c.1664C>T (p.Ala555Val)

gnomAD frequency: 0.00009  dbSNP: rs187814037
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen RCV001522504 SCV005382650 likely benign T-cell immunodeficiency, congenital alopecia, and nail dystrophy 2024-07-29 reviewed by expert panel curation The NM_001369369.1(FOXN1):c.1664C>T (p.Ala555Val) missense variant has a gnomADv2.1.1 PopMax filtering AF of 0.003187 based on 77/19952 alleles in the East Asian population, which is above the >0.00141 threshold for BS1. No deleterious effect is predicted with a REVEL score of 0.197 meeting the threshold of <0.290 for BP4. Additionally, no splicing effect is predicted by SpliceAI (delta score 0.00). After a comprehensive literature search, the variant has not been identified in any individuals with T-cell immunodeficiency, congenital alopecia, and nail dystrophy. In summary, this variant meets criteria to be classified as likely benign for semidominant T-cell immunodeficiency, congenital alopecia, and nail dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: BS1, BP4.
Labcorp Genetics (formerly Invitae), Labcorp RCV001522504 SCV001732065 benign T-cell immunodeficiency, congenital alopecia, and nail dystrophy 2024-01-31 criteria provided, single submitter clinical testing

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