Variant: NM_002185.5(IL7R):c.339A>C (p.Glu113Asp)

CA3231920

377977 (ClinVar)

Gene: IL7R

Condition: severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive

Inheritance Mode: Autosomal recessive inheritance

UUID: 61c2e4f6-db45-4b7d-ae0f-b21e30b896f9

Approved on: 2024-01-10

Published on: 2024-01-10

HGVS expressions

NM_002185.5:c.339A>C
NM_002185.5(IL7R):c.339A>C (p.Glu113Asp)
NC_000005.10:g.35867423A>C
CM000667.2:g.35867423A>C
NC_000005.9:g.35867525A>C
CM000667.1:g.35867525A>C
NC_000005.8:g.35903282A>C
NG_009567.1:g.15535A>C
ENST00000303115.8:c.339A>C
ENST00000303115.7:c.339A>C
ENST00000506850.5:c.339A>C
ENST00000511031.1:n.473A>C
ENST00000511982.1:c.339A>C
ENST00000514217.5:c.339A>C
NM_002185.3:c.339A>C
NR_120485.1:n.442A>C
NM_002185.4:c.339A>C
NR_120485.2:n.468A>C
NR_120485.3:n.426A>C

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 IL7R Version 1.0.0

Evidence submitted by expert panel

Severe Combined Immunodeficiency Disease VCEP

NM_002185.5(IL7R):c.339A>C is a missense variant predicted to cause substitution of Glutamic Acid by Aspartic Acid at amino acid 113 (p.Glu113Asp). The filtering allele frequency (the lower threshold of the 95% CI of 308/75016) of the c.339A>C variant in IL7R is 0.003481 for African/African American chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00126) for BS1, and therefore meets this criterion (BS1). To our knowledge, this variant has not been reported in the literature in individuals affected with IL7R-related conditions or in functional studies. In summary, this variant meets the criteria to be classified as Likely Benign variant for autosomal recessive severe combined immunodeficiency due to IL7R deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: BS1_met (VCEP specifications version 1).

Met criteria codes

• BS1: The filtering allele frequency (the lower threshold of the 95% CI of 308/75016) of the c.339A>C variant in IL7R is 0.003481 for African/African American chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00126) for BS1, and therefore meets this criterion (BS1).