rs17561
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
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 (no stars). 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1A | NM_000575.5 | c.340G>T | p.Ala114Ser | missense_variant | 5/7 | ENST00000263339.4 | NP_000566.3 | |
IL1A | NM_001371554.1 | c.340G>T | p.Ala114Ser | missense_variant | 5/7 | NP_001358483.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1A | ENST00000263339.4 | c.340G>T | p.Ala114Ser | missense_variant | 5/7 | 1 | NM_000575.5 | ENSP00000263339 | 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, no assertion criteria provided | 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