Variant chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002839.4(PTPRD):c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 1,606,216 control chromosomes in the GnomAD database, including 2,441 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.047 ( 209 hom., cov: 0)

Exomes 𝑓: 0.045 ( 2232 hom. )

Consequence

PTPRD
NM_002839.4 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.111

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 -10 ACMG points.

BP6

Variant 9-8331574-A-AAACTTACCATTCTTGAACTGTAACT is Benign according to our data. Variant chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACT is described in ClinVar as [Benign]. Clinvar id is 227045.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 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+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT		splice_region_variant, 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+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT		splice_region_variant, intron_variant		5	NM_002839.4	ENSP00000370593	P1	P23468-1

Frequencies

GnomAD3 genomes

AF:

0.0466

AC:

7082

AN:

151890

Hom.:

207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0423

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.0517

Gnomad ASJ

AF:

0.0392

Gnomad EAS

AF:

0.0311

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0469

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0419

Gnomad OTH

AF:

0.0495

GnomAD4 exome

AF:

0.0449

AC:

65343

AN:

1454212

Hom.:

2232

Cov.:

AF XY:

0.0481

AC XY:

34834

AN XY:

723618

show subpopulations

Gnomad4 AFR exome

AF:

0.0405

Gnomad4 AMR exome

AF:

0.0543

Gnomad4 ASJ exome

AF:

0.0335

Gnomad4 EAS exome

AF:

0.0346

Gnomad4 SAS exome

AF:

0.139

Gnomad4 FIN exome

AF:

0.0471

Gnomad4 NFE exome

AF:

0.0374

Gnomad4 OTH exome

AF:

0.0508

GnomAD4 genome

AF:

0.0468

AC:

7108

AN:

152004

Hom.:

209

Cov.:

AF XY:

0.0499

AC XY:

3707

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.0427

Gnomad4 AMR

AF:

0.0519

Gnomad4 ASJ

AF:

0.0392

Gnomad4 EAS

AF:

0.0312

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.0469

Gnomad4 NFE

AF:

0.0419

Gnomad4 OTH

AF:

0.0499

Alfa

AF:

0.0328

Hom.:

255

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Apr 03, 2015

c.5534+7_5534+8ins25 in intron 44 of PTPRD: This variant is not expected to have clinical significance because it has been identified in 15% (2409/16470) South Asian chromosomes, including 184 homozygotes, by the Exome Aggregation Consortiu m Sequencing Project (http://exac.broadinstitute.org/variant/9-8331574-A-AAACTTA CCATTCTTGAACTGTAACT; dbSNP rs3215098). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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