3-10219687-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001570.4(IRAK2):c.911C>T(p.Ser304Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,612,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001570.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRAK2 | NM_001570.4 | c.911C>T | p.Ser304Leu | missense_variant | 8/13 | ENST00000256458.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRAK2 | ENST00000256458.5 | c.911C>T | p.Ser304Leu | missense_variant | 8/13 | 1 | NM_001570.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152060Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250930Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135636
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1460798Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 726736
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152060Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.911C>T (p.S304L) alteration is located in exon 8 (coding exon 8) of the IRAK2 gene. This alteration results from a C to T substitution at nucleotide position 911, causing the serine (S) at amino acid position 304 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at