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.83-2A>T

CA10624373

353259 (ClinVar)

Gene: IL7R
Condition: severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive
Inheritance Mode: Autosomal recessive inheritance
UUID: 8f3d1796-3887-4b6d-a85a-7efb4571e6ee
Approved on: 2024-01-17
Published on: 2024-01-17

HGVS expressions

NM_002185.5:c.83-2A>T
NM_002185.5(IL7R):c.83-2A>T
NC_000005.10:g.35860850A>T
CM000667.2:g.35860850A>T
NC_000005.9:g.35860952A>T
CM000667.1:g.35860952A>T
NC_000005.8:g.35896709A>T
NG_009567.1:g.8962A>T
ENST00000303115.8:c.83-2A>T
ENST00000303115.7:c.83-2A>T
ENST00000506850.5:c.83-2A>T
ENST00000508941.5:c.83-2A>T
ENST00000511031.1:n.217-2A>T
ENST00000511982.1:c.83-2A>T
ENST00000514217.5:c.83-2A>T
ENST00000515665.1:c.83-2A>T
NM_002185.3:c.83-2A>T
NR_120485.1:n.186-2A>T
NM_002185.4:c.83-2A>T
NR_120485.2:n.212-2A>T
NR_120485.3:n.170-2A>T
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Pathogenic

Met criteria codes 3
PM3_Supporting PM2_Supporting PVS1
Not Met criteria codes 1
PP4

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 NM_002185.5(IL7R):c.83-2A>T variant occurs within the canonical splice acceptor site of intron 1. It is predicted to cause skipping of biologically relevant exon 2, resulting in a frameshift with a premature stop codon in exon 3/8, leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). Patient P4, of PMID: 15661025, is homozygous for this variant (PM3_supporting). At least four probands have been reported in the literature with this variant; however, insufficient information was available to apply PP4 (PMIDs: 32888943, 24578017, 21664875, 15661025). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00005649 (2/35406 alleles) in the Latino/Admixed American population, which is lower than the ClinGen SCID VCEP threshold (<0.00004129; PM2_Supporting). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PVS1, PM2_supporting, PM3_supporting. (SCID VCEP specifications version 1.0).
Met criteria codes
PM3_Supporting
P4 of PMID: 15661025 is homozygous for this variant (0.5pt; PM3_supporting). Additional compound heterozygotes have been reported but second variants have not yet been curated.
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00005649 (2/35406 alleles) in the Latino/Admixed American population (insufficient allele counts are available to calculate a filtering allele frequency), which is lower than the ClinGen SCID VCEP threshold (<0.00004129; PM2_Supporting).
PVS1
The NM_002185.5(IL7R):c.83-2A>T variant occurs within the canonical splice acceptor site of intron 1. It is predicted to cause skipping of biologically-relevant-exon 2, resulting in a frameshift with a premature stop codon in exon 3/8, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Not Met criteria codes
PP4
At least four probands have been reported in the literature with this variant, however insufficient information was available to apply PP4 (PMIDs: 32888943, 24578017, 21664875, 15661025).
Curation History
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