rs4807711

Variant names:

• chr19-5290344-C-G
• rs4807711
• NM_002850.4:c.-94-4110G>C

Variant summary

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

The NM_002850.4(PTPRS):​c.-94-4110G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,212 control chromosomes in the GnomAD database, including 3,277 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 0.19 (3277 hom., cov: 33)
• Consequence: PTPRS NM_002850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002850.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRS	NM_002850.4	MANE Select	c.-94-4110G>C		intron	N/A	NP_002841.3
	PTPRS	NM_001394011.1		c.-94-4110G>C		intron	N/A	NP_001380940.1
	PTPRS	NM_001394012.1		c.-94-4110G>C		intron	N/A	NP_001380941.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRS	ENST00000262963.11	TSL:5 MANE Select	c.-94-4110G>C		intron	N/A	ENSP00000262963.8	Q13332-1
	PTPRS	ENST00000588552.5	TSL:1	n.141-4110G>C		intron	N/A
	PTPRS	ENST00000919618.1		c.-94-4110G>C		intron	N/A	ENSP00000589677.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28580 AN: 152094 Hom.: 3268 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.188 AC: 28619 AN: 152212 Hom.: 3277 Cov.: 33 AF XY: 0.188 AC XY: 14001 AN XY: 74432

African (AFR) AF: 0.295 AC: 12252 AN: 41530

American (AMR) AF: 0.263 AC: 4021 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.113 AC: 586 AN: 5170

South Asian (SAS) AF: 0.149 AC: 720 AN: 4832

European-Finnish (FIN) AF: 0.105 AC: 1117 AN: 10622

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9021 AN: 67982

Other (OTH) AF: 0.179 AC: 378 AN: 2112

Alfa AF: 0.164 Hom.: 304

Bravo AF: 0.203

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.47
PhyloP100		-1.6
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: rs4807711; hg19: chr19-5290355;