rs11878779

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002850.4(PTPRS):​c.718+1401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,148 control chromosomes in the GnomAD database, including 4,865 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 0.22 ( 4865 hom., cov: 32)

Consequence

PTPRS
NM_002850.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.26
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTPRSNM_002850.4 linkuse as main transcriptc.718+1401C>T intron_variant ENST00000262963.11 NP_002841.3 Q13332-1Q8NHS7Q59FX6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTPRSENST00000262963.11 linkuse as main transcriptc.718+1401C>T intron_variant 5 NM_002850.4 ENSP00000262963.8 Q13332-1G8JL96

Frequencies

GnomAD3 genomes
AF:
0.222
AC:
33750
AN:
152028
Hom.:
4867
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0678
Gnomad AMI
AF:
0.354
Gnomad AMR
AF:
0.223
Gnomad ASJ
AF:
0.263
Gnomad EAS
AF:
0.00771
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.329
Gnomad OTH
AF:
0.256
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.222
AC:
33737
AN:
152148
Hom.:
4865
Cov.:
32
AF XY:
0.214
AC XY:
15929
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.0676
Gnomad4 AMR
AF:
0.222
Gnomad4 ASJ
AF:
0.263
Gnomad4 EAS
AF:
0.00772
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.329
Gnomad4 OTH
AF:
0.256
Alfa
AF:
0.280
Hom.:
1567
Bravo
AF:
0.216
Asia WGS
AF:
0.111
AC:
385
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.0040
DANN
Benign
0.64

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11878779; hg19: chr19-5254718; API