Genetic Variant PTPRQ:p.Thr33Ile (chr12-80444784-C-T) – ACMG Classification: Benign (-20 pts)

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

Genomes: 𝑓 0.032 ( 131 hom., cov: 32)

Exomes 𝑓: 0.026 ( 826 hom. )

Consequence

PTPRQ
NM_001145026.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 4.11

Variant links:

Genes affected

PTPRQ (HGNC:9679): (protein tyrosine phosphatase receptor type Q) This locus encodes a member of the type III receptor-like protein-tyrosine phosphatase family. The encoded protein catalyzes the dephosphorylation of phosphotyrosine and phosphatidylinositol and plays roles in cellular proliferation and differentiation. Mutations at this locus have been linked to autosomal recessive deafness. [provided by RefSeq, Mar 2014]

PTPRQ links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0025488138).

BP6

Variant 12-80444784-C-T is Benign according to our data. Variant chr12-80444784-C-T is described in ClinVar as [Benign]. Clinvar id is 508621.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRQ	NM_001145026.2 link	c.98C>T	p.Thr33Ile	missense_variant	Exon 2 of 45	ENST00000644991.3	NP_001138498.1	A0A087WZU1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRQ	ENST00000644991.3 link	c.98C>T	p.Thr33Ile	missense_variant	Exon 2 of 45		NM_001145026.2	ENSP00000495607.1		A0A087WZU1

Frequencies

GnomAD3 genomes

AF:

0.0322

AC:

4885

AN:

151738

Hom.:

130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0323

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0759

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.0541

Gnomad SAS

AF:

0.0870

Gnomad FIN

AF:

0.0337

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0183

Gnomad OTH

AF:

0.0206

GnomAD3 exomes

AF:

0.0456

AC:

6999

AN:

153410

Hom.:

293

AF XY:

0.0466

AC XY:

3795

AN XY:

81408

show subpopulations

Gnomad AFR exome

AF:

0.0382

Gnomad AMR exome

AF:

0.0944

Gnomad ASJ exome

AF:

0.0136

Gnomad EAS exome

AF:

0.0513

Gnomad SAS exome

AF:

0.0866

Gnomad FIN exome

AF:

0.0340

Gnomad NFE exome

AF:

0.0181

Gnomad OTH exome

AF:

0.0322

GnomAD4 exome

AF:

0.0256

AC:

35520

AN:

1387670

Hom.:

826

Cov.:

AF XY:

0.0271

AC XY:

18554

AN XY:

684630

show subpopulations

Gnomad4 AFR exome

AF:

0.0315

Gnomad4 AMR exome

AF:

0.0912

Gnomad4 ASJ exome

AF:

0.0140

Gnomad4 EAS exome

AF:

0.0560

Gnomad4 SAS exome

AF:

0.0830

Gnomad4 FIN exome

AF:

0.0317

Gnomad4 NFE exome

AF:

0.0181

Gnomad4 OTH exome

AF:

0.0264

GnomAD4 genome

AF:

0.0322

AC:

4894

AN:

151856

Hom.:

131

Cov.:

AF XY:

0.0351

AC XY:

2603

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.0324

Gnomad4 AMR

AF:

0.0759

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.0538

Gnomad4 SAS

AF:

0.0872

Gnomad4 FIN

AF:

0.0337

Gnomad4 NFE

AF:

0.0183

Gnomad4 OTH

AF:

0.0204

Alfa

AF:

0.0198

Hom.:

Bravo

AF:

0.0338

TwinsUK

AF:

0.0186

AC:

ALSPAC

AF:

0.0176

AC:

ESP6500AA

AF:

0.0311

AC:

ESP6500EA

AF:

0.0192

AC:

ExAC

AF:

0.0462

AC:

999

Asia WGS

AF:

0.0600

AC:

209

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Dec 06, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

May 09, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.055

T;T;T;T;.;.

Eigen

Uncertain

0.34

Eigen_PC

Benign

0.21

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.74

T;T;T;T;.;T

MetaRNN

Benign

0.0025

T;T;T;T;T;T

MetaSVM

Benign

-0.75

PrimateAI

Uncertain

0.57

PROVEAN

Uncertain

-3.1

D;D;D;.;.;.

REVEL

Uncertain

0.36

Sift

Uncertain

0.014

D;T;D;.;.;.

Sift4G

Pathogenic

0.0

D;D;D;D;D;.

Vest4

0.17, 0.57

ClinPred

0.012

GERP RS

4.9

gMVP

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over