Variant rs2278341 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001109754.4(PTPRB):c.4993+30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 1,603,946 control chromosomes in the GnomAD database, including 105,205 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 ( 9886 hom., cov: 32)

Exomes 𝑓: 0.36 ( 95319 hom. )

Consequence

PTPRB
NM_001109754.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.988

Variant links:

Genes affected

PTPRB (HGNC:9665): (protein tyrosine phosphatase receptor type B) 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 domain, a single transmembrane segment and one intracytoplasmic catalytic domain, thus belongs to receptor type PTP. The extracellular region of this PTP is composed of multiple fibronectin type_III repeats, which was shown to interact with neuronal receptor and cell adhesion molecules, such as contactin and tenascin C. This protein was also found to interact with sodium channels, and thus may regulate sodium channels by altering tyrosine phosphorylation status. The functions of the interaction partners of this protein implicate the roles of this PTP in cell adhesion, neurite growth, and neuronal differentiation. Alternate transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

PTPRB links:

LOC105369828 (HGNC:):

LOC105369828 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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRB	NM_001109754.4 linkuse as main transcript	c.4993+30C>T		intron_variant		ENST00000334414.11
LOC105369828	XR_001749196.2 linkuse as main transcript	n.10007-2140G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRB	ENST00000334414.11 linkuse as main transcript	c.4993+30C>T		intron_variant		1	NM_001109754.4	A1	P23467-3

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54135

AN:

151866

Hom.:

9885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.345

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.322

GnomAD3 exomes

AF:

0.334

AC:

81156

AN:

242796

Hom.:

14113

AF XY:

0.337

AC XY:

44431

AN XY:

131682

show subpopulations

Gnomad AFR exome

AF:

0.397

Gnomad AMR exome

AF:

0.245

Gnomad ASJ exome

AF:

0.300

Gnomad EAS exome

AF:

0.206

Gnomad SAS exome

AF:

0.359

Gnomad FIN exome

AF:

0.419

Gnomad NFE exome

AF:

0.354

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.359

AC:

521930

AN:

1451962

Hom.:

95319

Cov.:

AF XY:

0.359

AC XY:

258879

AN XY:

721266

show subpopulations

Gnomad4 AFR exome

AF:

0.396

Gnomad4 AMR exome

AF:

0.246

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.360

Gnomad4 FIN exome

AF:

0.416

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.354

GnomAD4 genome

AF:

0.356

AC:

54152

AN:

151984

Hom.:

9886

Cov.:

AF XY:

0.354

AC XY:

26330

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.298

Gnomad4 EAS

AF:

0.193

Gnomad4 SAS

AF:

0.345

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.342

Hom.:

9431

Bravo

AF:

0.346

Asia WGS

AF:

0.272

AC:

944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.6

DANN

Benign

0.77

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