chr1-198665496-T-C

Position:

• chr1-198665496-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002838.5(PTPRC):​c.73+26155T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,752 control chromosomes in the GnomAD database, including 19,758 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19758 hom., cov: 30)
• Consequence: PTPRC NM_002838.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRC	NM_002838.5	c.73+26155T>C		intron_variant		ENST00000442510.8	NP_002829.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRC	ENST00000442510.8	c.73+26155T>C		intron_variant		1	NM_002838.5	ENSP00000411355.3

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76519 AN: 151634 Hom.: 19743 Cov.: 30

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.528

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.505 AC: 76564 AN: 151752 Hom.: 19758 Cov.: 30 AF XY: 0.505 AC XY: 37471 AN XY: 74142

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.533

Alfa AF: 0.523 Hom.: 35145

Bravo AF: 0.502

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0030
DANN	Benign	0.34

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: rs1052238; hg19: chr1-198634625;