The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000448.3(RAG1):c.577G>A (p.Glu193Lys)

CA5950009

304495 (ClinVar)

Gene: RAG1
Condition: recombinase activating gene 1 deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: cb12f728-a219-4fd7-978f-b87b9a154e56
Approved on: 2024-01-17
Published on: 2024-01-17

HGVS expressions

NM_000448.3:c.577G>A
NM_000448.3(RAG1):c.577G>A (p.Glu193Lys)
NC_000011.10:g.36573881G>A
CM000673.2:g.36573881G>A
NC_000011.9:g.36595431G>A
CM000673.1:g.36595431G>A
NC_000011.8:g.36552007G>A
NG_007528.1:g.10869G>A
ENST00000299440.6:c.577G>A
ENST00000299440.5:c.577G>A
ENST00000534663.1:c.577G>A
NM_000448.2:c.577G>A
NM_001377277.1:c.577G>A
NM_001377278.1:c.577G>A
NM_001377279.1:c.577G>A
NM_001377280.1:c.577G>A
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Benign

Met criteria codes 2
BA1 BS2_Supporting

Evidence Links 0

Expert Panel

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
The c.577G>A (NM_000448.3) variant in RAG1 is a missense variant predicted to cause the substitution of Glutamic Acid by Lysine at amino acid 193 (p.Glu193Lys). The filtering allele frequency (the lower threshold of the 95% CI of 772/30614) of the c.577G>A variant in RAG1 is 0.02374 for South Asian chromosomes by gnomAD v2.1.1, which is higher than the ClinGen SCID VCEP threshold (>0.00872) for BA1, and therefore meets this criterion (BA1). 12 adult homozygous reported on GnomAD v2.1.1, BS2_Supporting is Met. In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG/AMP criteria applied, BA1 and BS2_Supporting, as specified by the ClinGen SCID VCEP (VCEP specifications version 1).
Met criteria codes
BA1
The filtering allele frequency (the lower threshold of the 95% CI of 772/30614) of the c.577G>A variant in RAG1 is 0.02374 for South Asian chromosomes by gnomAD v2.1.1, which is higher than the ClinGen SCID VCEP threshold (>0.00872) for BA1, and therefore meets this criterion (BA1).
BS2_Supporting
12 adult homozygous reported on GnomAD v2.1.1, BS2_Supporting is Met.
Curation History
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