rs12610082

Variant names:

• chr19-5226997-C-A
• rs12610082
• NM_002850.4:c.2377-1153G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-5226997-C-A
• chr19-5226997-C-G
• chr19-5226997-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002850.4(PTPRS):​c.2377-1153G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 151,918 control chromosomes in the GnomAD database, including 54,149 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 0.84 (54149 hom., cov: 28)
• Consequence: PTPRS NM_002850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRS	NM_002850.4	c.2377-1153G>T		intron_variant	Intron 16 of 37	ENST00000262963.11	NP_002841.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRS	ENST00000262963.11	c.2377-1153G>T		intron_variant	Intron 16 of 37	5	NM_002850.4	ENSP00000262963.8

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127603 AN: 151802 Hom.: 54106 Cov.: 28

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.841 AC: 127698 AN: 151918 Hom.: 54149 Cov.: 28 AF XY: 0.837 AC XY: 62107 AN XY: 74234

African (AFR) AF: 0.958 AC: 39720 AN: 41448

American (AMR) AF: 0.791 AC: 12075 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2670 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3702 AN: 5144

South Asian (SAS) AF: 0.751 AC: 3592 AN: 4786

European-Finnish (FIN) AF: 0.798 AC: 8422 AN: 10556

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54851 AN: 67934

Other (OTH) AF: 0.835 AC: 1765 AN: 2114

Alfa AF: 0.820 Hom.: 127386

Bravo AF: 0.846

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.35
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12610082; hg19: chr19-5227008;