rs973117

Variant names:

• chr9-9000033-C-A
• rs973117
• NM_002839.4:c.-104+18664G>T

Variant summary

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

The NM_002839.4(PTPRD):​c.-104+18664G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,826 control chromosomes in the GnomAD database, including 17,526 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 0.46 (17526 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-104+18664G>T		intron_variant	Intron 11 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-104+18664G>T		intron_variant	Intron 11 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-104+18664G>T		intron_variant	Intron 12 of 16	1		ENSP00000417661.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70091 AN: 151710 Hom.: 17495 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.462 AC: 70171 AN: 151826 Hom.: 17526 Cov.: 32 AF XY: 0.466 AC XY: 34565 AN XY: 74164

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.426

Alfa AF: 0.375 Hom.: 23305

Bravo AF: 0.484

Asia WGS AF: 0.519 AC: 1803 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.63

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: rs973117; hg19: chr9-9000033;