Variant: NM_000448.3(RAG1):c.486T>A (p.Asp162Glu)

CA5949991

879138 (ClinVar)

Gene: RAG1

Condition: recombinase activating gene 1 deficiency

Inheritance Mode: Autosomal recessive inheritance

UUID: b44c7d1f-dc1f-42fd-8a80-43ce32db161c

Approved on: 2024-02-07

Published on: 2024-02-07

HGVS expressions

NM_000448.3:c.486T>A
NM_000448.3(RAG1):c.486T>A (p.Asp162Glu)
NC_000011.10:g.36573790T>A
CM000673.2:g.36573790T>A
NC_000011.9:g.36595340T>A
CM000673.1:g.36595340T>A
NC_000011.8:g.36551916T>A
NG_007528.1:g.10778T>A
ENST00000697713.1:c.486T>A
ENST00000697714.1:c.486T>A
ENST00000697715.1:c.486T>A
ENST00000299440.6:c.486T>A
ENST00000299440.5:c.486T>A
ENST00000534663.1:c.486T>A
NM_000448.2:c.486T>A
NM_001377277.1:c.486T>A
NM_001377278.1:c.486T>A
NM_001377279.1:c.486T>A
NM_001377280.1:c.486T>A

Likely Benign

• Met criteria codes: BS1

Expert Panel

Severe Combined Immunodeficiency Disease VCEP

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAG1 Version 1.0.0

Evidence submitted by expert panel

Severe Combined Immunodeficiency Disease VCEP

NM_000448.3(RAG1):c.486T>A is a missense variant predicted to cause substitution of Aspartic Acid by Glutamic Acid at amino acid 162 (p.Asp162Glu). The filtering allele frequency (the upper threshold of the 95% CI of 113/44866 of the c.486T>A variant in RAG1 is 0.002166 for East Asian population, which is higher than the ClinGen SCID VCEP threshold (>0.001951) for BS1, and therefore meets this criterion (BS1). There are no publications for this variant in the literature. As per SCID VCEP specifications 1 Strong criteria is enough to reach Likely Benign classification. In summary, this variant meets the criteria to be classified as Likely Benign variant for autosomal recessive severe combined immunodeficiency due to RAG1 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: BS1 (VCEP specifications version 1).

Met criteria codes

• BS1: The filtering allele frequency (the upper threshold of the 95% CI of 113/44866 of the c.486T>A variant in RAG1 is 0.002166 for East Asian population, which is higher than the ClinGen SCID VCEP threshold (>0.001951) for BS1, and therefore meets this criterion (BS1).