X-154013378-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001569.4(IRAK1):c.1595C>T(p.Ser532Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_001569.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.732 AC: 81784AN: 111738Hom.: 22197 Cov.: 24 AF XY: 0.717 AC XY: 24354AN XY: 33944
GnomAD3 exomes AF: 0.674 AC: 110671AN: 164305Hom.: 26813 AF XY: 0.681 AC XY: 38591AN XY: 56707
GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.800 AC: 870719AN: 1088268Hom.: 246066 Cov.: 41 AF XY: 0.788 AC XY: 281652AN XY: 357396
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.732 AC: 81802AN: 111794Hom.: 22192 Cov.: 24 AF XY: 0.717 AC XY: 24385AN XY: 34010
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 61% of patients studied by a panel of primary immunodeficiencies. Number of patients: 58. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at