Variant 19-5206764-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002850.4(PTPRS):c.*10T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 1,611,932 control chromosomes in the GnomAD database, including 537,587 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 0.85 ( 55848 hom., cov: 33)

Exomes 𝑓: 0.81 ( 481739 hom. )

Consequence

PTPRS
NM_002850.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.331

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]

PTPRS links:

PTPRS (HGNC:):

PTPRS links:

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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=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRS	NM_002850.4 linkuse as main transcript	c.*10T>C		3_prime_UTR_variant	38/38	ENST00000262963.11	NP_002841.3	Q13332-1Q8NHS7Q59FX6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRS	ENST00000262963 linkuse as main transcript	c.*10T>C		3_prime_UTR_variant	38/38	5	NM_002850.4	ENSP00000262963.8		Q13332-1G8JL96

Frequencies

GnomAD3 genomes

AF:

0.852

AC:

129643

AN:

152080

Hom.:

55799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.963

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.803

Gnomad ASJ

AF:

0.827

Gnomad EAS

AF:

0.662

Gnomad SAS

AF:

0.789

Gnomad FIN

AF:

0.834

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.821

Gnomad OTH

AF:

0.842

GnomAD3 exomes

AF:

0.808

AC:

201079

AN:

249002

Hom.:

81692

AF XY:

0.805

AC XY:

108406

AN XY:

134704

show subpopulations

Gnomad AFR exome

AF:

0.965

Gnomad AMR exome

AF:

0.780

Gnomad ASJ exome

AF:

0.813

Gnomad EAS exome

AF:

0.678

Gnomad SAS exome

AF:

0.777

Gnomad FIN exome

AF:

0.816

Gnomad NFE exome

AF:

0.821

Gnomad OTH exome

AF:

0.813

GnomAD4 exome

AF:

0.811

AC:

1183773

AN:

1459734

Hom.:

481739

Cov.:

AF XY:

0.809

AC XY:

587922

AN XY:

726320

show subpopulations

Gnomad4 AFR exome

AF:

0.965

Gnomad4 AMR exome

AF:

0.787

Gnomad4 ASJ exome

AF:

0.814

Gnomad4 EAS exome

AF:

0.652

Gnomad4 SAS exome

AF:

0.777

Gnomad4 FIN exome

AF:

0.816

Gnomad4 NFE exome

AF:

0.816

Gnomad4 OTH exome

AF:

0.799

GnomAD4 genome

AF:

0.852

AC:

129744

AN:

152198

Hom.:

55848

Cov.:

AF XY:

0.850

AC XY:

63250

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.963

Gnomad4 AMR

AF:

0.802

Gnomad4 ASJ

AF:

0.827

Gnomad4 EAS

AF:

0.663

Gnomad4 SAS

AF:

0.788

Gnomad4 FIN

AF:

0.834

Gnomad4 NFE

AF:

0.821

Gnomad4 OTH

AF:

0.841

Alfa

AF:

0.826

Hom.:

42063

Bravo

AF:

0.856

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over