rs10759102

Positions:

• chr9-9910123-G-A
• chr9-9910123-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002839.4(PTPRD):​c.-368+28384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,562 control chromosomes in the GnomAD database, including 11,552 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 0.39 (11552 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRD	NM_002839.4	c.-368+28384C>T		intron_variant		ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9	c.-368+28384C>T		intron_variant		5	NM_002839.4	P1
PTPRD	ENST00000463477.5	c.-440+28384C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58310 AN: 151444 Hom.: 11523 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.386

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.385 AC: 58390 AN: 151562 Hom.: 11552 Cov.: 31 AF XY: 0.390 AC XY: 28893 AN XY: 74062

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.391

Alfa AF: 0.355 Hom.: 7752

Bravo AF: 0.387

Asia WGS AF: 0.506 AC: 1755 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs10759102; hg19: chr9-9910123;