rs146620441
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_139276.3(STAT3):āc.1492A>Gā(p.Ile498Val) variant causes a missense change. The variant allele was found at a frequency of 0.000167 in 1,614,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_139276.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000756 AC: 115AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000243 AC: 61AN: 251476Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135916
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461894Hom.: 0 Cov.: 34 AF XY: 0.000106 AC XY: 77AN XY: 727248
GnomAD4 genome AF: 0.000756 AC: 115AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000672 AC XY: 50AN XY: 74432
ClinVar
Submissions by phenotype
not specified Benign:1
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not provided Benign:1
STAT3: PP2, BP4, BS1 -
STAT3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hyper-IgE recurrent infection syndrome 1, autosomal dominant;C4288261:STAT3 gain of function Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at