rs3917320
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000877.4(IL1R1):āc.1366A>Cā(p.Arg456=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 1,614,118 control chromosomes in the GnomAD database, including 2,191 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.057 ( 310 hom., cov: 32)
Exomes š: 0.046 ( 1881 hom. )
Consequence
IL1R1
NM_000877.4 synonymous
NM_000877.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.101
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
?
Synonymous conserved (PhyloP=0.101 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0839 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1R1 | NM_000877.4 | c.1366A>C | p.Arg456= | synonymous_variant | 12/12 | ENST00000410023.6 | |
IL1R1-AS1 | NR_174960.1 | n.305+3497T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1R1 | ENST00000410023.6 | c.1366A>C | p.Arg456= | synonymous_variant | 12/12 | 1 | NM_000877.4 | P1 | |
IL1R1-AS1 | ENST00000428188.1 | n.305+3497T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0567 AC: 8634AN: 152198Hom.: 311 Cov.: 32
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GnomAD3 exomes AF: 0.0416 AC: 10443AN: 251320Hom.: 340 AF XY: 0.0404 AC XY: 5494AN XY: 135846
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GnomAD4 exome AF: 0.0463 AC: 67736AN: 1461800Hom.: 1881 Cov.: 32 AF XY: 0.0455 AC XY: 33078AN XY: 727198
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GnomAD4 genome ? AF: 0.0567 AC: 8642AN: 152318Hom.: 310 Cov.: 32 AF XY: 0.0552 AC XY: 4114AN XY: 74488
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ClinVar
Not reported inComputational 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