chr5-157248931-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005546.4(ITK):c.1715G>T(p.Ser572Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S572N) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITK | NM_005546.4 | c.1715G>T | p.Ser572Ile | missense_variant | 16/17 | ENST00000422843.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITK | ENST00000422843.8 | c.1715G>T | p.Ser572Ile | missense_variant | 16/17 | 1 | NM_005546.4 | P1 | |
ITK | ENST00000519749.1 | n.720G>T | non_coding_transcript_exon_variant | 5/6 | 1 | ||||
ITK | ENST00000519402.5 | n.3300G>T | non_coding_transcript_exon_variant | 15/16 | 2 | ||||
ITK | ENST00000696962.1 | c.*492G>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/16 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251094Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135704
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461612Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727122
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74458
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at