rs10514818

chr9-9865816-C-Achr9-9865816-C-T

Variant summary

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

The NM_002839.4(PTPRD):c.-368+72691G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,130 control chromosomes in the GnomAD database, including 1,278 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 0.084 (1278 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRD	NM_002839.4	c.-368+72691G>T		intron_variant		ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9	c.-368+72691G>T		intron_variant		5	NM_002839.4	P1
PTPRD	ENST00000463477.5	c.-440+72691G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12778 AN: 152012 Hom.: 1269 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0843 AC: 12826 AN: 152130 Hom.: 1278 Cov.: 32 AF XY: 0.0818 AC XY: 6083 AN XY: 74392

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0487

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.0194

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0244 Hom.: 37

Bravo AF: 0.0924

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.1
Dann	Benign	0.73

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

Other links and lift over

dbSNP: rs10514818; hg19: chr9-9865816;