rs12975955

Variant summary

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

The NM_002850.4(PTPRS):​c.3765+147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 946,482 control chromosomes in the GnomAD database, including 83,859 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 0.36 ( 10554 hom., cov: 33)
Exomes 𝑓: 0.42 ( 73305 hom. )

Consequence

PTPRS
NM_002850.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.727
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTPRSNM_002850.4 linkuse as main transcriptc.3765+147A>G intron_variant ENST00000262963.11 NP_002841.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTPRSENST00000262963.11 linkuse as main transcriptc.3765+147A>G intron_variant 5 NM_002850.4 ENSP00000262963 A1Q13332-1

Frequencies

GnomAD3 genomes
AF:
0.360
AC:
54672
AN:
151914
Hom.:
10550
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.221
Gnomad AMI
AF:
0.442
Gnomad AMR
AF:
0.327
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.592
Gnomad SAS
AF:
0.443
Gnomad FIN
AF:
0.377
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.426
Gnomad OTH
AF:
0.353
GnomAD4 exome
AF:
0.424
AC:
336818
AN:
794450
Hom.:
73305
AF XY:
0.425
AC XY:
171926
AN XY:
404400
show subpopulations
Gnomad4 AFR exome
AF:
0.214
Gnomad4 AMR exome
AF:
0.340
Gnomad4 ASJ exome
AF:
0.336
Gnomad4 EAS exome
AF:
0.573
Gnomad4 SAS exome
AF:
0.455
Gnomad4 FIN exome
AF:
0.375
Gnomad4 NFE exome
AF:
0.430
Gnomad4 OTH exome
AF:
0.399
GnomAD4 genome
AF:
0.360
AC:
54697
AN:
152032
Hom.:
10554
Cov.:
33
AF XY:
0.360
AC XY:
26745
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.221
Gnomad4 AMR
AF:
0.326
Gnomad4 ASJ
AF:
0.352
Gnomad4 EAS
AF:
0.592
Gnomad4 SAS
AF:
0.443
Gnomad4 FIN
AF:
0.377
Gnomad4 NFE
AF:
0.426
Gnomad4 OTH
AF:
0.355
Alfa
AF:
0.409
Hom.:
6039
Bravo
AF:
0.352
Asia WGS
AF:
0.436
AC:
1519
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.5
DANN
Benign
0.65

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: rs12975955; hg19: chr19-5219803; API