12-66211448-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_007199.3(IRAK3):āc.439A>Gā(p.Ile147Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,589,414 control chromosomes in the GnomAD database, including 652,620 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. 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_007199.3 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRAK3 | NM_007199.3 | c.439A>G | p.Ile147Val | missense_variant, splice_region_variant | 5/12 | ENST00000261233.9 | |
IRAK3 | NM_001142523.2 | c.256A>G | p.Ile86Val | missense_variant, splice_region_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRAK3 | ENST00000261233.9 | c.439A>G | p.Ile147Val | missense_variant, splice_region_variant | 5/12 | 1 | NM_007199.3 | P1 | |
IRAK3 | ENST00000457197.2 | c.256A>G | p.Ile86Val | missense_variant, splice_region_variant | 4/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.790 AC: 120057AN: 152054Hom.: 50509 Cov.: 32
GnomAD3 exomes AF: 0.872 AC: 218441AN: 250616Hom.: 97642 AF XY: 0.879 AC XY: 119179AN XY: 135570
GnomAD4 exome AF: 0.911 AC: 1308715AN: 1437242Hom.: 602094 Cov.: 29 AF XY: 0.911 AC XY: 652923AN XY: 716676
GnomAD4 genome AF: 0.789 AC: 120113AN: 152172Hom.: 50526 Cov.: 32 AF XY: 0.791 AC XY: 58830AN XY: 74408
ClinVar
Submissions by phenotype
IRAK3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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