Variant 9-8331548-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002839.4(PTPRD):c.5534+34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 1,028,882 control chromosomes in the GnomAD database, including 2,344 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.050 ( 170 hom., cov: 32)

Exomes 𝑓: 0.070 ( 2174 hom. )

Consequence

PTPRD
NM_002839.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.92

Variant links:

Genes affected

PTPRD (HGNC:9668): (protein tyrosine phosphatase receptor type D) 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 three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010]

PTPRD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 9-8331548-C-T is Benign according to our data. Variant chr9-8331548-C-T is described in ClinVar as [Benign]. Clinvar id is 1247371.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRD	NM_002839.4 linkuse as main transcript	c.5534+34G>A		intron_variant		ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9 linkuse as main transcript	c.5534+34G>A		intron_variant		5	NM_002839.4	ENSP00000370593	P1	P23468-1

Frequencies

GnomAD3 genomes

AF:

0.0499

AC:

5690

AN:

114118

Hom.:

171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0218

Gnomad AMI

AF:

0.0430

Gnomad AMR

AF:

0.0636

Gnomad ASJ

AF:

0.0462

Gnomad EAS

AF:

0.0394

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.0541

Gnomad MID

AF:

0.0667

Gnomad NFE

AF:

0.0476

Gnomad OTH

AF:

0.0547

GnomAD3 exomes

AF:

0.0823

AC:

12513

AN:

152068

Hom.:

533

AF XY:

0.0898

AC XY:

7544

AN XY:

84012

show subpopulations

Gnomad AFR exome

AF:

0.0387

Gnomad AMR exome

AF:

0.0996

Gnomad ASJ exome

AF:

0.0517

Gnomad EAS exome

AF:

0.0491

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.0616

Gnomad NFE exome

AF:

0.0572

Gnomad OTH exome

AF:

0.0797

GnomAD4 exome

AF:

0.0704

AC:

64408

AN:

914726

Hom.:

2174

Cov.:

AF XY:

0.0753

AC XY:

34457

AN XY:

457470

show subpopulations

Gnomad4 AFR exome

AF:

0.0404

Gnomad4 AMR exome

AF:

0.116

Gnomad4 ASJ exome

AF:

0.0522

Gnomad4 EAS exome

AF:

0.0655

Gnomad4 SAS exome

AF:

0.232

Gnomad4 FIN exome

AF:

0.0627

Gnomad4 NFE exome

AF:

0.0582

Gnomad4 OTH exome

AF:

0.0778

GnomAD4 genome

AF:

0.0500

AC:

5704

AN:

114156

Hom.:

170

Cov.:

AF XY:

0.0544

AC XY:

3030

AN XY:

55738

show subpopulations

Gnomad4 AFR

AF:

0.0222

Gnomad4 AMR

AF:

0.0638

Gnomad4 ASJ

AF:

0.0462

Gnomad4 EAS

AF:

0.0394

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.0541

Gnomad4 NFE

AF:

0.0476

Gnomad4 OTH

AF:

0.0555

Alfa

AF:

0.0383

Hom.:

Bravo

AF:

0.0343

Asia WGS

AF:

0.0890

AC:

307

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 29, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.10

DANN

Benign

0.32

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over