rs17561
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000575.5(IL1A):c.340G>T(p.Ala114Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,604,102 control chromosomes in the GnomAD database, including 67,974 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000575.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1A | NM_000575.5 | c.340G>T | p.Ala114Ser | missense_variant | 5/7 | ENST00000263339.4 | |
IL1A | NM_001371554.1 | c.340G>T | p.Ala114Ser | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1A | ENST00000263339.4 | c.340G>T | p.Ala114Ser | missense_variant | 5/7 | 1 | NM_000575.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.257 AC: 39015AN: 151936Hom.: 5326 Cov.: 32
GnomAD3 exomes AF: 0.270 AC: 67603AN: 250734Hom.: 9650 AF XY: 0.275 AC XY: 37261AN XY: 135534
GnomAD4 exome AF: 0.290 AC: 421059AN: 1452046Hom.: 62644 Cov.: 32 AF XY: 0.291 AC XY: 210151AN XY: 720964
GnomAD4 genome AF: 0.257 AC: 39041AN: 152056Hom.: 5330 Cov.: 32 AF XY: 0.259 AC XY: 19239AN XY: 74292
ClinVar
Submissions by phenotype
IL1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at