Variant rs17108344 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001109754.4(PTPRB):c.4419G>A(p.Ala1473=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00942 in 1,612,790 control chromosomes in the GnomAD database, including 524 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 0.033 ( 235 hom., cov: 32)

Exomes 𝑓: 0.0069 ( 289 hom. )

Consequence

PTPRB
NM_001109754.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP7

Synonymous conserved (PhyloP=-1.79 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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.4419G>A	p.Ala1473=	synonymous_variant	17/34	ENST00000334414.11
LOC105369828	XR_001749196.2 linkuse as main transcript	n.10185C>T		non_coding_transcript_exon_variant	8/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRB	ENST00000334414.11 linkuse as main transcript	c.4419G>A	p.Ala1473=	synonymous_variant	17/34	1	NM_001109754.4	A1	P23467-3

Frequencies

GnomAD3 genomes

AF:

0.0334

AC:

5052

AN:

151064

Hom.:

236

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0136

Gnomad ASJ

AF:

0.0194

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.0314

Gnomad FIN

AF:

0.0000945

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.00294

Gnomad OTH

AF:

0.0319

GnomAD3 exomes

AF:

0.0139

AC:

3453

AN:

249034

Hom.:

111

AF XY:

0.0135

AC XY:

1823

AN XY:

135106

show subpopulations

Gnomad AFR exome

AF:

0.106

Gnomad AMR exome

AF:

0.00722

Gnomad ASJ exome

AF:

0.0168

Gnomad EAS exome

AF:

0.000223

Gnomad SAS exome

AF:

0.0313

Gnomad FIN exome

AF:

0.0000929

Gnomad NFE exome

AF:

0.00304

Gnomad OTH exome

AF:

0.0132

GnomAD4 exome

AF:

0.00694

AC:

10138

AN:

1461608

Hom.:

289

Cov.:

AF XY:

0.00737

AC XY:

5360

AN XY:

727094

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.00763

Gnomad4 ASJ exome

AF:

0.0165

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0296

Gnomad4 FIN exome

AF:

0.000150

Gnomad4 NFE exome

AF:

0.00190

Gnomad4 OTH exome

AF:

0.0135

GnomAD4 genome

AF:

0.0334

AC:

5054

AN:

151182

Hom.:

235

Cov.:

AF XY:

0.0326

AC XY:

2410

AN XY:

73890

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.0136

Gnomad4 ASJ

AF:

0.0194

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.0315

Gnomad4 FIN

AF:

0.0000945

Gnomad4 NFE

AF:

0.00294

Gnomad4 OTH

AF:

0.0315

Alfa

AF:

0.0194

Hom.:

Bravo

AF:

0.0368

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.00491

EpiControl

AF:

0.00504

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

4.4

DANN

Benign

0.50

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