rs16929560

Positions:

• chr9-9474970-A-C
• chr9-9474970-A-G
• chr9-9474970-A-T

Variant summary

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

The NM_002839.4(PTPRD):​c.-236-77488T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,700 control chromosomes in the GnomAD database, including 26,605 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 0.59 (26605 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-236-77488T>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.-236-77488T>G		intron_variant		5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-308-60147T>G		intron_variant		1		ENSP00000417661.1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 88933 AN: 151580 Hom.: 26599 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.587 AC: 88982 AN: 151700 Hom.: 26605 Cov.: 31 AF XY: 0.589 AC XY: 43632 AN XY: 74120

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.622

Alfa AF: 0.619 Hom.: 56890

Bravo AF: 0.584

Asia WGS AF: 0.637 AC: 2212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.40

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: rs16929560; hg19: chr9-9474970;