Variant 12-80425096-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000547376.5(PTPRQ):c.205A>G(p.Arg69Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 454,882 control chromosomes in the GnomAD database, including 141,756 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.72 ( 41371 hom., cov: 32)

Exomes 𝑓: 0.81 ( 100385 hom. )

Consequence

PTPRQ
ENST00000547376.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:3

Conservation

PhyloP100: 2.68

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.0327069E-6).

BP6

Variant 12-80425096-A-G is Benign according to our data. Variant chr12-80425096-A-G is described in ClinVar as [Benign]. Clinvar id is 1174628.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-80425096-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein
PTPRQ	ENST00000547376.5 linkuse as main transcript	c.205A>G	p.Arg69Gly	missense_variant	6/12	5	ENSP00000448844
PTPRQ	ENST00000551042.5 linkuse as main transcript	c.205A>G	p.Arg69Gly	missense_variant	9/14	5	ENSP00000447522
PTPRQ	ENST00000551573.5 linkuse as main transcript	c.253A>G	p.Arg85Gly	missense_variant	4/9	3	ENSP00000449133

Frequencies

GnomAD3 genomes

AF:

0.717

AC:

108876

AN:

151902

Hom.:

41373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.446

Gnomad AMI

AF:

0.790

Gnomad AMR

AF:

0.695

Gnomad ASJ

AF:

0.844

Gnomad EAS

AF:

0.771

Gnomad SAS

AF:

0.824

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.854

Gnomad OTH

AF:

0.762

GnomAD3 exomes

AF:

0.773

AC:

98246

AN:

127130

Hom.:

38924

AF XY:

0.788

AC XY:

54841

AN XY:

69614

show subpopulations

Gnomad AFR exome

AF:

0.419

Gnomad AMR exome

AF:

0.626

Gnomad ASJ exome

AF:

0.848

Gnomad EAS exome

AF:

0.760

Gnomad SAS exome

AF:

0.831

Gnomad FIN exome

AF:

0.792

Gnomad NFE exome

AF:

0.852

Gnomad OTH exome

AF:

0.801

GnomAD4 exome

AF:

0.808

AC:

244731

AN:

302862

Hom.:

100385

Cov.:

AF XY:

0.816

AC XY:

140776

AN XY:

172480

show subpopulations

Gnomad4 AFR exome

AF:

0.432

Gnomad4 AMR exome

AF:

0.627

Gnomad4 ASJ exome

AF:

0.844

Gnomad4 EAS exome

AF:

0.761

Gnomad4 SAS exome

AF:

0.829

Gnomad4 FIN exome

AF:

0.795

Gnomad4 NFE exome

AF:

0.854

Gnomad4 OTH exome

AF:

0.801

GnomAD4 genome

AF:

0.716

AC:

108899

AN:

152020

Hom.:

41371

Cov.:

AF XY:

0.714

AC XY:

53074

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.446

Gnomad4 AMR

AF:

0.695

Gnomad4 ASJ

AF:

0.844

Gnomad4 EAS

AF:

0.771

Gnomad4 SAS

AF:

0.823

Gnomad4 FIN

AF:

0.787

Gnomad4 NFE

AF:

0.854

Gnomad4 OTH

AF:

0.762

Alfa

AF:

0.806

Hom.:

13247

Bravo

AF:

0.693

TwinsUK

AF:

0.846

AC:

3137

ALSPAC

AF:

0.857

AC:

3303

ExAC

AF:

0.798

AC:

9662

Asia WGS

AF:

0.780

AC:

2708

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.055

T;T;T

Eigen

Benign

-0.13

Eigen_PC

Benign

-0.18

FATHMM_MKL

Uncertain

0.85

LIST_S2

Benign

0.42

T;T;T

MetaRNN

Benign

0.0000010

T;T;T

MetaSVM

Benign

-1.1

PROVEAN

Benign

-1.7

N;D;N

REVEL

Benign

0.086

Sift

Benign

0.46

T;D;T

Sift4G

Pathogenic

0.0

D;D;D

ClinPred

0.015

GERP RS

4.2

Splicing

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