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.778G>A (p.Ala260Thr)

CA3232088

418258 (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: b7f37408-9259-49ff-bee4-1506448289b1
Approved on: 2024-01-17
Published on: 2024-01-17

HGVS expressions

NM_002185.5:c.778G>A
NM_002185.5(IL7R):c.778G>A (p.Ala260Thr)
NC_000005.10:g.35874520G>A
CM000667.2:g.35874520G>A
NC_000005.9:g.35874622G>A
CM000667.1:g.35874622G>A
NC_000005.8:g.35910379G>A
NG_009567.1:g.22632G>A
ENST00000303115.8:c.778G>A
ENST00000303115.7:c.778G>A
ENST00000505093.1:c.115+872G>A
ENST00000506850.5:c.706+872G>A
ENST00000509668.1:n.520G>A
ENST00000514217.5:c.538-992G>A
NM_002185.3:c.778G>A
NR_120485.1:n.641-992G>A
NM_002185.4:c.778G>A
NR_120485.2:n.667-992G>A
NR_120485.3:n.625-992G>A
More

Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 1
BS2

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.778G>A (NM_002185.5) variant in IL7R is a missense variant predicted to cause substitution of Alanine by Threonine at amino acid 260 (p.Ala260Thr). The filtering allele frequency (the lower threshold of the 95% CI of 115/24962) of the c.778G>A variant in IL7R is 0.003885 in exomes and 0.003267 in genomes (no homozygous reported) for African/African American chromosomes by gnomAD v2.1.1. Both values are higher than the ClinGen SCID VCEP threshold (0.00126) for BS1 and therefore meet this criterion (BS1). The variant has not been identified in the literature. In summary, this variant meets the criteria to be classified as Likely Benign for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: BS1. (VCEP specifications version 1).
Met criteria codes
BS1
The filtering allele frequency (the lower threshold of the 95% CI of 115/24962) of the c.778G>A variant in IL7R is 0.003885 in exomes and 0.003267 in genomes (no homozygous reported) for African/African American chromosomes by gnomAD v2.1.1. Both values are higher than the ClinGen SCID VCEP threshold (0.00126) for BS1 and therefore meet this criterion (BS1).
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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