rs9854688
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001570.4(IRAK2):c.1507C>A(p.Leu503Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,614,118 control chromosomes in the GnomAD database, including 586 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001570.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRAK2 | NM_001570.4 | c.1507C>A | p.Leu503Ile | missense_variant | 12/13 | ENST00000256458.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRAK2 | ENST00000256458.5 | c.1507C>A | p.Leu503Ile | missense_variant | 12/13 | 1 | NM_001570.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0373 AC: 5668AN: 152150Hom.: 278 Cov.: 32
GnomAD3 exomes AF: 0.0131 AC: 3296AN: 251354Hom.: 128 AF XY: 0.0113 AC XY: 1538AN XY: 135860
GnomAD4 exome AF: 0.00752 AC: 10996AN: 1461852Hom.: 308 Cov.: 32 AF XY: 0.00735 AC XY: 5347AN XY: 727230
GnomAD4 genome ? AF: 0.0373 AC: 5676AN: 152266Hom.: 278 Cov.: 32 AF XY: 0.0361 AC XY: 2691AN XY: 74446
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at