rs2230611

chr19-5212471-G-Achr19-5212471-G-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_002850.4(PTPRS):c.4635C>T(p.Arg1545=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,593,162 control chromosomes in the GnomAD database, including 12,169 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 0.12 (1278 hom., cov: 33)
  • Exomes 𝑓: 0.12 (10891 hom.)
• Consequence: PTPRS NM_002850.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.78

Genes affected

PTPRS (HGNC:9681): (protein tyrosine phosphatase receptor type S) 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, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of multiple Ig-like and fibronectin type III-like domains. Studies of the similar gene in mice suggested that this PTP may be involved in cell-cell interaction, primary axonogenesis, and axon guidance during embryogenesis. This PTP has been also implicated in the molecular control of adult nerve repair. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP7: Synonymous conserved (PhyloP=-4.78 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRS	NM_002850.4	c.4635C>T	p.Arg1545=	synonymous_variant	31/38	ENST00000262963.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRS	ENST00000262963.11	c.4635C>T	p.Arg1545=	synonymous_variant	31/38	5	NM_002850.4	A1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18685 AN: 152088 Hom.: 1277 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.138

GnomAD3 exomes AF: 0.136 AC: 29287 AN: 214790 Hom.: 2433 AF XY: 0.132 AC XY: 15277 AN XY: 116152

Gnomad AFR exome AF: 0.107

Gnomad AMR exome AF: 0.279

Gnomad ASJ exome AF: 0.0968

Gnomad EAS exome AF: 0.0615

Gnomad SAS exome AF: 0.164

Gnomad FIN exome AF: 0.132

Gnomad NFE exome AF: 0.104

Gnomad OTH exome AF: 0.132

GnomAD4 exome AF: 0.118 AC: 169764 AN: 1440956 Hom.: 10891 Cov.: 35 AF XY: 0.118 AC XY: 84706 AN XY: 714950

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.0990

Gnomad4 EAS exome AF: 0.0685

Gnomad4 SAS exome AF: 0.165

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.119

GnomAD4 genome AF: 0.123 AC: 18692 AN: 152206 Hom.: 1278 Cov.: 33 AF XY: 0.125 AC XY: 9332 AN XY: 74408

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0688

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.137

Alfa AF: 0.111 Hom.: 1477

Bravo AF: 0.128

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	0.30
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2230611; hg19: chr19-5212482; COSMIC: COSV53614219; COSMIC: COSV53614219;