Variant 20-42085839-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_007050.6(PTPRT):c.3861C>T(p.Tyr1287=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,609,210 control chromosomes in the GnomAD database, including 42,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.20 ( 3252 hom., cov: 32)

Exomes 𝑓: 0.23 ( 39552 hom. )

Consequence

PTPRT
NM_007050.6 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.99

Variant links:

Genes affected

PTPRT (HGNC:9682): (protein tyrosine phosphatase receptor type T) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

PTPRT links:

LOC101927182 (HGNC:):

LOC101927182 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 20-42085839-G-A is Benign according to our data. Variant chr20-42085839-G-A is described in ClinVar as [Benign]. Clinvar id is 3060307.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=2.99 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRT	NM_007050.6 linkuse as main transcript	c.3861C>T	p.Tyr1287=	synonymous_variant	28/31	ENST00000373187.6
LOC101927182	XR_001754611.2 linkuse as main transcript	n.378-4740G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRT	ENST00000373187.6 linkuse as main transcript	c.3861C>T	p.Tyr1287=	synonymous_variant	28/31	1	NM_007050.6	P4	O14522-3

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30137

AN:

152068

Hom.:

3253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.278

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.0708

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.197

AC:

48991

AN:

249234

Hom.:

5298

AF XY:

0.201

AC XY:

27117

AN XY:

135220

show subpopulations

Gnomad AFR exome

AF:

0.130

Gnomad AMR exome

AF:

0.138

Gnomad ASJ exome

AF:

0.270

Gnomad EAS exome

AF:

0.0764

Gnomad SAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.199

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.211

GnomAD4 exome

AF:

0.227

AC:

331332

AN:

1457024

Hom.:

39552

Cov.:

AF XY:

0.227

AC XY:

164359

AN XY:

725130

show subpopulations

Gnomad4 AFR exome

AF:

0.132

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.267

Gnomad4 EAS exome

AF:

0.0719

Gnomad4 SAS exome

AF:

0.165

Gnomad4 FIN exome

AF:

0.195

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.198

AC:

30138

AN:

152186

Hom.:

3252

Cov.:

AF XY:

0.194

AC XY:

14454

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.0704

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.195

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.228

Hom.:

2984

Bravo

AF:

0.194

Asia WGS

AF:

0.105

AC:

366

AN:

3478

EpiCase

AF:

0.255

EpiControl

AF:

0.262

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PTPRT-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

9.7

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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