9-10430602-T-C

Position:

• chr9-10430602-T-C

Variant summary

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

The NM_002839.4(PTPRD):​c.-599-89585A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,740 control chromosomes in the GnomAD database, including 14,724 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 0.37 (14724 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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 = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-599-89585A>G		intron_variant		ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-599-89585A>G		intron_variant		5	NM_002839.4	ENSP00000370593	P1
PTPRD	ENST00000463477.5	c.-671-89585A>G		intron_variant		1		ENSP00000417661

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56618 AN: 151624 Hom.: 14679 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.374 AC: 56721 AN: 151740 Hom.: 14724 Cov.: 32 AF XY: 0.379 AC XY: 28084 AN XY: 74118

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.348

Alfa AF: 0.228 Hom.: 11284

Bravo AF: 0.409

Asia WGS AF: 0.587 AC: 2012 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs649891; hg19: chr9-10430602;