Variant 9-8389364-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002839.4(PTPRD):c.4254G>C(p.Gly1418=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 1,611,518 control chromosomes in the GnomAD database, including 168,428 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 19402 hom., cov: 31)

Exomes 𝑓: 0.45 ( 149026 hom. )

Consequence

PTPRD
NM_002839.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.274

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 9-8389364-C-G is Benign according to our data. Variant chr9-8389364-C-G is described in ClinVar as [Benign]. Clinvar id is 1225000.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.274 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRD	NM_002839.4 linkuse as main transcript	c.4254G>C	p.Gly1418=	synonymous_variant	37/46	ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9 linkuse as main transcript	c.4254G>C	p.Gly1418=	synonymous_variant	37/46	5	NM_002839.4	P1	P23468-1

Frequencies

GnomAD3 genomes

AF:

0.498

AC:

75512

AN:

151622

Hom.:

19374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.582

Gnomad AMI

AF:

0.641

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.659

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.486

GnomAD3 exomes

AF:

0.495

AC:

123709

AN:

249724

Hom.:

31459

AF XY:

0.496

AC XY:

66963

AN XY:

135044

show subpopulations

Gnomad AFR exome

AF:

0.585

Gnomad AMR exome

AF:

0.490

Gnomad ASJ exome

AF:

0.460

Gnomad EAS exome

AF:

0.673

Gnomad SAS exome

AF:

0.566

Gnomad FIN exome

AF:

0.490

Gnomad NFE exome

AF:

0.442

Gnomad OTH exome

AF:

0.472

GnomAD4 exome

AF:

0.448

AC:

654647

AN:

1459778

Hom.:

149026

Cov.:

AF XY:

0.451

AC XY:

327711

AN XY:

726250

show subpopulations

Gnomad4 AFR exome

AF:

0.590

Gnomad4 AMR exome

AF:

0.489

Gnomad4 ASJ exome

AF:

0.460

Gnomad4 EAS exome

AF:

0.619

Gnomad4 SAS exome

AF:

0.553

Gnomad4 FIN exome

AF:

0.491

Gnomad4 NFE exome

AF:

0.425

Gnomad4 OTH exome

AF:

0.467

GnomAD4 genome

AF:

0.498

AC:

75602

AN:

151740

Hom.:

19402

Cov.:

AF XY:

0.505

AC XY:

37426

AN XY:

74174

show subpopulations

Gnomad4 AFR

AF:

0.583

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.659

Gnomad4 SAS

AF:

0.565

Gnomad4 FIN

AF:

0.492

Gnomad4 NFE

AF:

0.433

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.448

Hom.:

5123

Bravo

AF:

0.502

Asia WGS

AF:

0.599

AC:

2081

AN:

3476

EpiCase

AF:

0.440

EpiControl

AF:

0.442

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	Oct 22, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

3.5

DANN

Benign

0.70

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