Variant 20-42079239-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007050.6(PTPRT):c.*1640G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 208,086 control chromosomes in the GnomAD database, including 4,718 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3317 hom., cov: 33)

Exomes 𝑓: 0.21 ( 1401 hom. )

Consequence

PTPRT
NM_007050.6 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0670

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 20-42079239-C-T is Benign according to our data. Variant chr20-42079239-C-T is described in ClinVar as [Benign]. Clinvar id is 1285993.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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.*1640G>A		3_prime_UTR_variant	31/31	ENST00000373187.6
LOC101927182	XR_001754611.2 linkuse as main transcript	n.378-11340C>T		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.*1640G>A		3_prime_UTR_variant	31/31	1	NM_007050.6	P4	O14522-3

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30517

AN:

152078

Hom.:

3318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.0700

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.210

AC:

11714

AN:

55890

Hom.:

1401

Cov.:

AF XY:

0.211

AC XY:

5448

AN XY:

25864

show subpopulations

Gnomad4 AFR exome

AF:

0.143

Gnomad4 AMR exome

AF:

0.157

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.0628

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.248

Gnomad4 OTH exome

AF:

0.224

GnomAD4 genome

AF:

0.201

AC:

30518

AN:

152196

Hom.:

3317

Cov.:

AF XY:

0.198

AC XY:

14701

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.201

Gnomad4 ASJ

AF:

0.280

Gnomad4 EAS

AF:

0.0696

Gnomad4 SAS

AF:

0.169

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.246

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.240

Hom.:

4559

Bravo

AF:

0.196

Asia WGS

AF:

0.107

AC:

374

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 18, 2020

This variant is associated with the following publications: (PMID: 25967969) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.5

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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