NM_001145026.2:c.202G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001145026.2(PTPRQ):c.202G>A(p.Gly68Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00161 in 1,547,432 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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.202G>A | p.Gly68Arg | missense_variant | Exon 3 of 45 | ENST00000644991.3 | NP_001138498.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRQ | ENST00000644991.3 | c.202G>A | p.Gly68Arg | missense_variant | Exon 3 of 45 | NM_001145026.2 | ENSP00000495607.1 |
Frequencies
GnomAD3 genomes AF: 0.00318 AC: 482AN: 151640Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00914 AC: 1384AN: 151376Hom.: 44 AF XY: 0.00659 AC XY: 530AN XY: 80396
GnomAD4 exome AF: 0.00143 AC: 1993AN: 1395674Hom.: 56 Cov.: 30 AF XY: 0.00119 AC XY: 817AN XY: 688350
GnomAD4 genome AF: 0.00331 AC: 502AN: 151758Hom.: 17 Cov.: 32 AF XY: 0.00348 AC XY: 258AN XY: 74188
ClinVar
Submissions by phenotype
not specified Benign:2
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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. -
not provided Benign:2
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PTPRQ-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at