Variant 1-198638984-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2

The ENST00000348564.11(PTPRC):c.-197C>T variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00158 in 395,272 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 6 hom., cov: 32)

Exomes 𝑓: 0.00050 ( 2 hom. )

Consequence

PTPRC
ENST00000348564.11 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.97

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BP6

Variant 1-198638984-C-T is Benign according to our data. Variant chr1-198638984-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1212714.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0033 (502/152144) while in subpopulation AFR AF= 0.0107 (446/41504). AF 95% confidence interval is 0.00992. There are 6 homozygotes in gnomad4. There are 234 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
PTPRC	XM_047426381.1 linkuse as main transcript	c.-44+198C>T	intron_variant	XP_047282337.1
PTPRC	XM_047426398.1 linkuse as main transcript	c.-44+198C>T	intron_variant	XP_047282354.1
PTPRC	XM_047426409.1 linkuse as main transcript	c.-44+198C>T	intron_variant	XP_047282365.1
PTPRC	XM_047426415.1 linkuse as main transcript	c.-44+198C>T	intron_variant	XP_047282371.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	Appris	UniProt
PTPRC	ENST00000348564.11 linkuse as main transcript	c.-197C>T	5_prime_UTR_variant	1/30	1	ENSP00000306782	P2	P08575-4
PTPRC	ENST00000367379.6 linkuse as main transcript	c.-43-242C>T	intron_variant		5	ENSP00000356349
PTPRC	ENST00000643513.1 linkuse as main transcript	c.-44+198C>T	intron_variant			ENSP00000494132
PTPRC	ENST00000530727.5 linkuse as main transcript		upstream_gene_variant		1	ENSP00000433536

Frequencies

GnomAD3 genomes

AF:

0.00331

AC:

503

AN:

152026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0108

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00315

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00288

GnomAD4 exome

AF:

0.000502

AC:

122

AN:

243128

Hom.:

Cov.:

AF XY:

0.000455

AC XY:

AN XY:

129586

show subpopulations

Gnomad4 AFR exome

AF:

0.0123

Gnomad4 AMR exome

AF:

0.00110

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000405

Gnomad4 OTH exome

AF:

0.000985

GnomAD4 genome

AF:

0.00330

AC:

502

AN:

152144

Hom.:

Cov.:

AF XY:

0.00315

AC XY:

234

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0107

Gnomad4 AMR

AF:

0.00315

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.00229

Hom.:

Bravo

AF:

0.00393

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely 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

-0.25

CADD

Benign

DANN

Benign

0.97

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