chr5-157181063-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_005546.4(ITK):c.86G>A(p.Arg29His) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R29C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005546.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITK | NM_005546.4 | c.86G>A | p.Arg29His | missense_variant | 1/17 | ENST00000422843.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITK | ENST00000422843.8 | c.86G>A | p.Arg29His | missense_variant | 1/17 | 1 | NM_005546.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251158Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135758
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727152
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Lymphoproliferative syndrome 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at