rs13019803
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000877.4(IL1R1):c.61+1957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,138 control chromosomes in the GnomAD database, including 2,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.14 ( 2116 hom., cov: 32)
Consequence
IL1R1
NM_000877.4 intron
NM_000877.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.305
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1R1 | NM_000877.4 | c.61+1957C>T | intron_variant | ENST00000410023.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1R1 | ENST00000410023.6 | c.61+1957C>T | intron_variant | 1 | NM_000877.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21349AN: 152020Hom.: 2111 Cov.: 32
GnomAD3 genomes
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152020
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.141 AC: 21386AN: 152138Hom.: 2116 Cov.: 32 AF XY: 0.141 AC XY: 10463AN XY: 74386
GnomAD4 genome
?
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AC:
21386
AN:
152138
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32
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AC XY:
10463
AN XY:
74386
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Asia WGS
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429
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3478
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Ascending aortic dissection Other:1
association, no assertion criteria provided | case-control | Beijing Anzhen Hospital, Capital Medical University | Feb 01, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at