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]

Variant: NM_002185.5(IL7R):c.1043A>C (p.Asn348Thr)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA160111

134532 (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: d6943a2d-65f3-453d-8466-d14040885cb4

Approved on: 2024-04-03

Published on: 2024-04-03

HGVS expressions

NM_002185.5:c.1043A>C

NM_002185.5(IL7R):c.1043A>C (p.Asn348Thr)

NC_000005.10:g.35876149A>C

CM000667.2:g.35876149A>C

NC_000005.9:g.35876251A>C

CM000667.1:g.35876251A>C

NC_000005.8:g.35912008A>C

NG_009567.1:g.24261A>C

ENST00000303115.8:c.1043A>C

ENST00000303115.7:c.1043A>C

ENST00000505093.1:c.358A>C

ENST00000505875.1:n.341A>C

ENST00000514217.5:c.*237A>C

NM_002185.3:c.1043A>C

NR_120485.1:n.883A>C

NM_002185.4:c.1043A>C

NR_120485.2:n.909A>C

NR_120485.3:n.867A>C

Benign

BS2_Supporting BA1

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

The c.1043A>C (NM_002185.5) variant in IL7R is a missense variant predicted to cause substitution of Asparagine by Threonine at amino acid 348 (p.Asn348Thr). The filtering allele frequency (the lower threshold of the 95% CI of 20801/1179968 alleles) of the c.1043A>C variant in IL7R is 0.01743 for European (non-Finnish) chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00566) for BA1, and therefore meets this criterion (BA1). Additionally, 215 adult homozygous occurrences are described in gnomAD (BS2_Supporting). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: BA1 and BS2_Supporting. (VCEP specifications version 1)

BS2_Supporting

Additionally, 215 adult homozygous occurrences are described in gnomAD (BS2_Supporting).

BA1

The filtering allele frequency (the lower threshold of the 95% CI of 20801/1179968 alleles) of the c.1043A>C variant in IL7R is 0.01743 for European (non-Finnish) chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00566) for BA1, and therefore meets this criterion (BA1).

Curation History

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