Evidence Repository - Clinical Genome Resources

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

Link to SEPIO compliant JSON-LD document

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

Link to MONDO

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

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

BS1

Evidence Links 0

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

Criteria Specification Approval History

Criteria Specifications for this VCEP

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).

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).

Approved on: 2024-01-10

Published on: 2024-01-10

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.