Evidence Repository
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.731C>T (p.Thr244Ile)

CA160105

134530 (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: 2276fa62-1e5a-4e37-82d0-ca41c4b6b94d
Approved on: 2024-01-23
Published on: 2024-01-23

HGVS expressions

NM_002185.5:c.731C>T
NM_002185.5(IL7R):c.731C>T (p.Thr244Ile)
NC_000005.10:g.35874473C>T
CM000667.2:g.35874473C>T
NC_000005.9:g.35874575C>T
CM000667.1:g.35874575C>T
NC_000005.8:g.35910332C>T
NG_009567.1:g.22585C>T
ENST00000303115.8:c.731C>T
ENST00000303115.7:c.731C>T
ENST00000505093.1:c.115+825C>T
ENST00000506850.5:c.706+825C>T
ENST00000509668.1:n.473C>T
ENST00000514217.5:c.538-1039C>T
NM_002185.3:c.731C>T
NR_120485.1:n.641-1039C>T
NM_002185.4:c.731C>T
NR_120485.2:n.667-1039C>T
NR_120485.3:n.625-1039C>T
More

Benign

Met criteria codes 2
BS2_Supporting BA1

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 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.731C>T (NM_002185.5) variant in IL7R is a missense variant predicted to cause substitution of Threonine by Isoleucine at amino acid 244 (p.Thr244Ile). The filtering allele frequency (the lower threshold of the 95% CI of 21695/63972 alleles) of the c.731C>T variant in IL7R is 0.2678 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, 53760 homozygous adults are reported in gnomAD v.4. 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, as specified by the ClinGen SCID-VCEP: BA1 and BS2_Supporting. (VCEP specifications version 1).
Met criteria codes
BS2_Supporting
Additionally, 53760 homozygous adults are reported in gnomAD v.4. BS2_Supporting is Met.
BA1
The filtering allele frequency (the lower threshold of the 95% CI of 21695/63972 alleles) of the c.731C>T variant in IL7R is 0.2678 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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