rs9292618
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002185.5(IL7R):c.*1924G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 232,966 control chromosomes in the GnomAD database, including 2,066 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1318 hom., cov: 33)
Exomes 𝑓: 0.13 ( 748 hom. )
Consequence
IL7R
NM_002185.5 3_prime_UTR
NM_002185.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.61
Genes affected
IL7R (HGNC:6024): (interleukin 7 receptor) The protein encoded by this gene is a receptor for interleukin 7 (IL7). The function of this receptor requires the interleukin 2 receptor, gamma chain (IL2RG), which is a common gamma chain shared by the receptors of various cytokines, including interleukins 2, 4, 7, 9, and 15. This protein has been shown to play a critical role in V(D)J recombination during lymphocyte development. Defects in this gene may be associated with severe combined immunodeficiency (SCID). Alternatively spliced transcript variants have been found. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 5-35878410-G-A is Benign according to our data. Variant chr5-35878410-G-A is described in ClinVar as [Benign]. Clinvar id is 353301.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL7R | NM_002185.5 | c.*1924G>A | 3_prime_UTR_variant | 8/8 | ENST00000303115.8 | ||
IL7R | NM_001410734.1 | c.*2421G>A | 3_prime_UTR_variant | 7/7 | |||
IL7R | NR_120485.3 | n.3128G>A | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL7R | ENST00000303115.8 | c.*1924G>A | 3_prime_UTR_variant | 8/8 | 1 | NM_002185.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.131 AC: 19948AN: 152060Hom.: 1318 Cov.: 33
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GnomAD4 exome AF: 0.134 AC: 10808AN: 80788Hom.: 748 Cov.: 0 AF XY: 0.134 AC XY: 4968AN XY: 37124
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GnomAD4 genome ? AF: 0.131 AC: 19940AN: 152178Hom.: 1318 Cov.: 33 AF XY: 0.128 AC XY: 9513AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunodeficiency 104 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at