chr3-10209666-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001570.4(IRAK2):c.502G>A(p.Asp168Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000671 in 1,550,526 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001570.4 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 |
---|---|---|---|---|---|---|---|
IRAK2 | NM_001570.4 | c.502G>A | p.Asp168Asn | missense_variant | 4/13 | ENST00000256458.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRAK2 | ENST00000256458.5 | c.502G>A | p.Asp168Asn | missense_variant | 4/13 | 1 | NM_001570.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000490 AC: 10AN: 204248Hom.: 0 AF XY: 0.0000535 AC XY: 6AN XY: 112228
GnomAD4 exome AF: 0.0000644 AC: 90AN: 1398396Hom.: 1 Cov.: 30 AF XY: 0.0000605 AC XY: 42AN XY: 694770
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74374
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at