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]

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Variant: NM_002185.5(IL7R):c.412G>A (p.Val138Ile)

CA124393

14840 (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: 08ce9006-62e7-4115-8b9f-3378119517cb

HGVS expressions

NM_002185.5:c.412G>A

NM_002185.5(IL7R):c.412G>A (p.Val138Ile)

NC_000005.10:g.35871088G>A

CM000667.2:g.35871088G>A

NC_000005.9:g.35871190G>A

CM000667.1:g.35871190G>A

NC_000005.8:g.35906947G>A

NG_009567.1:g.19200G>A

ENST00000303115.8:c.412G>A

ENST00000303115.7:c.412G>A

ENST00000506850.5:c.412G>A

ENST00000514217.5:c.412G>A

NM_002185.3:c.412G>A

NR_120485.1:n.515G>A

NM_002185.4:c.412G>A

NR_120485.2:n.541G>A

NR_120485.3:n.499G>A

Benign

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

NM_002185.5(IL7R):c.412G>A is a missense variant predicted to cause substitution of Valine by Isoleucine at amino acid 138 (p.Val138Ile). The filtering allele frequency (the lower threshold of the 95% CI of 65661/74940 alleles) of the c.412G>A variant in IL7R is 0.8743 for African/African American chromosomes by gnomAD v.4, which is higher than the ClinGen SCID VCEP threshold (>0.00566) for BA1 and therefore meets this criterion (BA1). Additionally, 367924 homozygous have been described. 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. Criteria applied: BA1 (VCEP specifications version 1).

BA1

The filtering allele frequency (the lower threshold of the 95% CI of 65661/74940 alleles) of the c.412G>A variant in IL7R is 0.8743 for African/African American chromosomes by gnomAD v.4, which is higher than the ClinGen SCID VCEP threshold (>0.00566) for BA1 and therefore meets this criterion (BA1). Additionally, 367924 homozygous have been described.

Approved on: 2024-01-23

Published on: 2024-01-23

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