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.152C>T (p.Ser51Leu)

CA160084

134523 (ClinVar)

Gene: IL7R
Condition: severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive
Inheritance Mode: Autosomal recessive inheritance
UUID: 156db031-c96a-41bc-bf7e-69a6fc4103ae
Approved on: 2024-01-10
Published on: 2024-01-10

HGVS expressions

NM_002185.5:c.152C>T
NM_002185.5(IL7R):c.152C>T (p.Ser51Leu)
NC_000005.10:g.35860921C>T
CM000667.2:g.35860921C>T
NC_000005.9:g.35861023C>T
CM000667.1:g.35861023C>T
NC_000005.8:g.35896780C>T
NG_009567.1:g.9033C>T
ENST00000303115.8:c.152C>T
ENST00000303115.7:c.152C>T
ENST00000506850.5:c.152C>T
ENST00000508941.5:c.152C>T
ENST00000511031.1:n.286C>T
ENST00000511982.1:c.152C>T
ENST00000514217.5:c.152C>T
ENST00000515665.1:c.152C>T
NM_002185.3:c.152C>T
NR_120485.1:n.255C>T
NM_002185.4:c.152C>T
NR_120485.2:n.281C>T
NR_120485.3:n.239C>T

Likely Benign

Met criteria codes 1
BS1

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
NM_002185.5(IL7R):c.152C>T is a missense variant predicted to cause substitution of Serine by Leucine at amino acid 51 (p.Ser51Leu). The filtering allele frequency (the lower threshold of the 95% CI of 110/74978) of the c.152C>T variant in IL7R is 0.001270 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. As per SCID VCEP specifications, 1 Strong criteria is enough to reach Likely Benign classification. In summary, this variant meets the criteria to be classified as a 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 (VCEP specifications version 1).
Met criteria codes
BS1
The filtering allele frequency (the lower threshold of the 95% CI of 110/74978) of the c.152C>T variant in IL7R is 0.001270 for African/African American chromosomes by gnomAD v2.1.1, which is higher than the ClinGen SCID VCEP threshold (>0.00126) for BS1, and therefore meets this criterion (BS1).
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