1-198694393-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000413409.6(PTPRC):c.*212C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 1,088,604 control chromosomes in the GnomAD database, including 170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.013 (22 hom., cov: 31)
  • Exomes 𝑓: 0.015 (148 hom.)
• Consequence: PTPRC ENST00000413409.6 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.305

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 1-198694393-C-T is Benign according to our data. Variant chr1-198694393-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1197008.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0129 (1967/152208) while in subpopulation NFE AF= 0.0161 (1092/68002). AF 95% confidence interval is 0.0153. There are 22 homozygotes in gnomad4. There are 1045 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRC	NM_002838.5	c.100+2020C>T		intron_variant		ENST00000442510.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRC	ENST00000442510.8	c.100+2020C>T		intron_variant		1	NM_002838.5	A2

Frequencies

GnomAD3 genomes AF: 0.0129 AC: 1966 AN: 152090 Hom.: 22 Cov.: 31

Gnomad AFR AF: 0.00229

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0161

Gnomad OTH AF: 0.0120

GnomAD4 exome AF: 0.0145 AC: 13586 AN: 936396 Hom.: 148 Cov.: 12 AF XY: 0.0143 AC XY: 6476 AN XY: 451800

Gnomad4 AFR exome AF: 0.00185

Gnomad4 AMR exome AF: 0.00767

Gnomad4 ASJ exome AF: 0.00254

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0117

Gnomad4 FIN exome AF: 0.0316

Gnomad4 NFE exome AF: 0.0154

Gnomad4 OTH exome AF: 0.0121

GnomAD4 genome AF: 0.0129 AC: 1967 AN: 152208 Hom.: 22 Cov.: 31 AF XY: 0.0140 AC XY: 1045 AN XY: 74418

Gnomad4 AFR AF: 0.00229

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.0482

Gnomad4 NFE AF: 0.0161

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.00726 Hom.: 0

Bravo AF: 0.00937

Asia WGS AF: 0.00693 AC: 25 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 05, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.5
Dann	Benign	0.27

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

Other links and lift over

dbSNP: rs12134940; hg19: chr1-198663522;