rs149047410
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000215.4(JAK3):c.1187C>T(p.Pro396Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00025 in 1,614,006 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000215.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAK3 | NM_000215.4 | c.1187C>T | p.Pro396Leu | missense_variant | 9/24 | ENST00000458235.7 | |
JAK3 | XM_047438786.1 | c.1187C>T | p.Pro396Leu | missense_variant | 9/24 | ||
JAK3 | XM_011527991.3 | c.1187C>T | p.Pro396Leu | missense_variant | 9/14 | ||
JAK3 | XR_007066796.1 | n.1237C>T | non_coding_transcript_exon_variant | 9/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAK3 | ENST00000458235.7 | c.1187C>T | p.Pro396Leu | missense_variant | 9/24 | 5 | NM_000215.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152152Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000526 AC: 132AN: 250838Hom.: 0 AF XY: 0.000678 AC XY: 92AN XY: 135708
GnomAD4 exome AF: 0.000261 AC: 382AN: 1461736Hom.: 1 Cov.: 31 AF XY: 0.000344 AC XY: 250AN XY: 727154
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152270Hom.: 0 Cov.: 30 AF XY: 0.000188 AC XY: 14AN XY: 74462
ClinVar
Submissions by phenotype
T-B+ severe combined immunodeficiency due to JAK3 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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