12-80444784-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001145026.2(PTPRQ):c.98C>T(p.Thr33Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0263 in 1,539,526 control chromosomes in the GnomAD database, including 957 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001145026.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRQ | NM_001145026.2 | c.98C>T | p.Thr33Ile | missense_variant | Exon 2 of 45 | ENST00000644991.3 | NP_001138498.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRQ | ENST00000644991.3 | c.98C>T | p.Thr33Ile | missense_variant | Exon 2 of 45 | NM_001145026.2 | ENSP00000495607.1 |
Frequencies
GnomAD3 genomes AF: 0.0322 AC: 4885AN: 151738Hom.: 130 Cov.: 32
GnomAD3 exomes AF: 0.0456 AC: 6999AN: 153410Hom.: 293 AF XY: 0.0466 AC XY: 3795AN XY: 81408
GnomAD4 exome AF: 0.0256 AC: 35520AN: 1387670Hom.: 826 Cov.: 30 AF XY: 0.0271 AC XY: 18554AN XY: 684630
GnomAD4 genome AF: 0.0322 AC: 4894AN: 151856Hom.: 131 Cov.: 32 AF XY: 0.0351 AC XY: 2603AN XY: 74230
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at