rs536358097
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000534444.1(JAK3):c.3280G>A(p.Ala1094Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000751 in 1,092,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Synonymous variant affecting the same amino acid position (i.e. A1094A) has been classified as Benign.
Frequency
Consequence
ENST00000534444.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAK3 | NM_000215.4 | c.3207+73G>A | intron_variant | ENST00000458235.7 | |||
JAK3 | XM_047438786.1 | c.3207+73G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAK3 | ENST00000458235.7 | c.3207+73G>A | intron_variant | 5 | NM_000215.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000347 AC: 48AN: 138342Hom.: 0 AF XY: 0.000358 AC XY: 27AN XY: 75446
GnomAD4 exome AF: 0.0000702 AC: 66AN: 939712Hom.: 0 Cov.: 13 AF XY: 0.0000769 AC XY: 37AN XY: 481420
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74496
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at