rs140634356
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_002185.5(IL7R):c.1200G>A(p.Val400=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,613,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00077 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000070 ( 0 hom. )
Consequence
IL7R
NM_002185.5 synonymous
NM_002185.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.120
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 -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 5-35876306-G-A is Benign according to our data. Variant chr5-35876306-G-A is described in ClinVar as [Benign]. Clinvar id is 533078.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.12 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000775 (118/152286) while in subpopulation AFR AF= 0.00274 (114/41552). AF 95% confidence interval is 0.00233. There are 0 homozygotes in gnomad4. There are 61 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL7R | NM_002185.5 | c.1200G>A | p.Val400= | synonymous_variant | 8/8 | ENST00000303115.8 | |
IL7R | NM_001410734.1 | c.*317G>A | 3_prime_UTR_variant | 7/7 | |||
IL7R | NR_120485.3 | n.1024G>A | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL7R | ENST00000303115.8 | c.1200G>A | p.Val400= | synonymous_variant | 8/8 | 1 | NM_002185.5 | P1 | |
IL7R | ENST00000505093.1 | c.*317G>A | 3_prime_UTR_variant | 3/3 | 2 | ||||
IL7R | ENST00000505875.1 | n.498G>A | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
IL7R | ENST00000514217.5 | c.*394G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000782 AC: 119AN: 152168Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000143 AC: 36AN: 251044Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135662
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GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461418Hom.: 0 Cov.: 33 AF XY: 0.0000578 AC XY: 42AN XY: 726914
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GnomAD4 genome ? AF: 0.000775 AC: 118AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000819 AC XY: 61AN XY: 74468
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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 | Invitae | Jan 04, 2024 | - - |
Computational scores
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Name
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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