Variant 1-198735165-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002838.5(PTPRC):c.2316C>T(p.Gly772Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,602,070 control chromosomes in the GnomAD database, including 18,709 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2562 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16147 hom. )

Consequence

PTPRC
NM_002838.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.704

Variant links:

Genes affected

PTPRC (HGNC:9666): (protein tyrosine phosphatase receptor type C) 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, mitosis, and oncogenic transformation. This PTP contains an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus is classified as a receptor type PTP. This PTP has been shown to be an essential regulator of T- and B-cell antigen receptor signaling. It functions through either direct interaction with components of the antigen receptor complexes, or by activating various Src family kinases required for the antigen receptor signaling. This PTP also suppresses JAK kinases, and thus functions as a regulator of cytokine receptor signaling. Alternatively spliced transcripts variants of this gene, which encode distinct isoforms, have been reported. [provided by RefSeq, Jun 2012]

PTPRC links:

PTPRC (HGNC:):

PTPRC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 1-198735165-C-T is Benign according to our data. Variant chr1-198735165-C-T is described in ClinVar as [Benign]. Clinvar id is 1166021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.704 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRC	NM_002838.5 linkuse as main transcript	c.2316C>T	p.Gly772Gly	synonymous_variant	23/33	ENST00000442510.8	NP_002829.3	P08575-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRC	ENST00000442510.8 linkuse as main transcript	c.2316C>T	p.Gly772Gly	synonymous_variant	23/33	1	NM_002838.5	ENSP00000411355.3		P08575-3

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25869

AN:

151374

Hom.:

2554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.0674

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.164

GnomAD3 exomes

AF:

0.169

AC:

42013

AN:

248794

Hom.:

4295

AF XY:

0.163

AC XY:

21953

AN XY:

134520

show subpopulations

Gnomad AFR exome

AF:

0.246

Gnomad AMR exome

AF:

0.289

Gnomad ASJ exome

AF:

0.0987

Gnomad EAS exome

AF:

0.257

Gnomad SAS exome

AF:

0.207

Gnomad FIN exome

AF:

0.0708

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.155

GnomAD4 exome

AF:

0.141

AC:

204127

AN:

1450576

Hom.:

16147

Cov.:

AF XY:

0.141

AC XY:

102068

AN XY:

721554

show subpopulations

Gnomad4 AFR exome

AF:

0.247

Gnomad4 AMR exome

AF:

0.290

Gnomad4 ASJ exome

AF:

0.101

Gnomad4 EAS exome

AF:

0.244

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.0750

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.171

AC:

25902

AN:

151494

Hom.:

2562

Cov.:

AF XY:

0.169

AC XY:

12500

AN XY:

74046

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.0674

Gnomad4 NFE

AF:

0.126

Gnomad4 OTH

AF:

0.165

Alfa

AF:

0.136

Hom.:

3066

Bravo

AF:

0.187

Asia WGS

AF:

0.229

AC:

792

AN:

3464

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Immunodeficiency 104

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

5.3

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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