chr2-102171877-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000877.4(IL1R1):c.798A>G(p.Val266=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000911 in 1,608,856 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0049 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00049 ( 5 hom. )
Consequence
IL1R1
NM_000877.4 synonymous
NM_000877.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.72
Genes affected
IL1R1 (HGNC:5993): (interleukin 1 receptor type 1) This gene encodes a cytokine receptor that belongs to the interleukin-1 receptor family. The encoded protein is a receptor for interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist. It is an important mediator involved in many cytokine-induced immune and inflammatory responses. This gene is located in a cluster of related cytokine receptor genes on chromosome 2q12. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 2-102171877-A-G is Benign according to our data. Variant chr2-102171877-A-G is described in ClinVar as [Benign]. Clinvar id is 711343.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.72 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00493 (750/152226) while in subpopulation AFR AF= 0.0174 (724/41528). AF 95% confidence interval is 0.0164. There are 4 homozygotes in gnomad4. There are 334 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 749 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1R1 | NM_000877.4 | c.798A>G | p.Val266= | synonymous_variant | 8/12 | ENST00000410023.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1R1 | ENST00000410023.6 | c.798A>G | p.Val266= | synonymous_variant | 8/12 | 1 | NM_000877.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00492 AC: 749AN: 152108Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00111 AC: 278AN: 250696Hom.: 1 AF XY: 0.000723 AC XY: 98AN XY: 135524
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GnomAD4 exome AF: 0.000492 AC: 716AN: 1456630Hom.: 5 Cov.: 28 AF XY: 0.000399 AC XY: 289AN XY: 724686
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 15, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at