Variant chr1-198694217-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000413409.6(PTPRC):c.*36G>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 0.0599 in 1,395,476 control chromosomes in the GnomAD database, including 2,855 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 275 hom., cov: 31)

Exomes 𝑓: 0.062 ( 2580 hom. )

Consequence

PTPRC
ENST00000413409.6 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.508

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 1-198694217-G-A is Benign according to our data. Variant chr1-198694217-G-A is described in ClinVar as [Benign]. Clinvar id is 1277649.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRC	NM_002838.5 linkuse as main transcript	c.100+1844G>A		intron_variant		ENST00000442510.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRC	ENST00000442510.8 linkuse as main transcript	c.100+1844G>A		intron_variant		1	NM_002838.5	A2	P08575-3

Frequencies

GnomAD3 genomes

AF:

0.0463

AC:

7020

AN:

151628

Hom.:

275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0104

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.0224

Gnomad ASJ

AF:

0.0260

Gnomad EAS

AF:

0.000389

Gnomad SAS

AF:

0.0336

Gnomad FIN

AF:

0.0982

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0695

Gnomad OTH

AF:

0.0359

GnomAD3 exomes

AF:

0.0534

AC:

2798

AN:

52352

Hom.:

103

AF XY:

0.0554

AC XY:

1545

AN XY:

27872

show subpopulations

Gnomad AFR exome

AF:

0.0111

Gnomad AMR exome

AF:

0.0178

Gnomad ASJ exome

AF:

0.0263

Gnomad EAS exome

AF:

0.000633

Gnomad SAS exome

AF:

0.0362

Gnomad FIN exome

AF:

0.0938

Gnomad NFE exome

AF:

0.0642

Gnomad OTH exome

AF:

0.0374

GnomAD4 exome

AF:

0.0616

AC:

76607

AN:

1243730

Hom.:

2580

Cov.:

AF XY:

0.0612

AC XY:

37068

AN XY:

605920

show subpopulations

Gnomad4 AFR exome

AF:

0.00894

Gnomad4 AMR exome

AF:

0.0176

Gnomad4 ASJ exome

AF:

0.0303

Gnomad4 EAS exome

AF:

0.000310

Gnomad4 SAS exome

AF:

0.0366

Gnomad4 FIN exome

AF:

0.0955

Gnomad4 NFE exome

AF:

0.0668

Gnomad4 OTH exome

AF:

0.0494

GnomAD4 genome

AF:

0.0462

AC:

7016

AN:

151746

Hom.:

275

Cov.:

AF XY:

0.0463

AC XY:

3428

AN XY:

74108

show subpopulations

Gnomad4 AFR

AF:

0.0104

Gnomad4 AMR

AF:

0.0224

Gnomad4 ASJ

AF:

0.0260

Gnomad4 EAS

AF:

0.000390

Gnomad4 SAS

AF:

0.0337

Gnomad4 FIN

AF:

0.0982

Gnomad4 NFE

AF:

0.0695

Gnomad4 OTH

AF:

0.0355

Alfa

AF:

0.0564

Hom.:

Bravo

AF:

0.0376

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 06, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.51

DANN

Benign

0.72

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