rs9332452

Variant names:

• chr9-9393975-T-C
• rs9332452
• NM_002839.4:c.-203+3474A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002839.4(PTPRD):​c.-203+3474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,942 control chromosomes in the GnomAD database, including 25,317 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 0.57 (25317 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-203+3474A>G		intron_variant	Intron 9 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-203+3474A>G		intron_variant	Intron 9 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-203+3474A>G		intron_variant	Intron 10 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-203+3474A>G		intron_variant	Intron 11 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86725 AN: 151824 Hom.: 25301 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.571 AC: 86783 AN: 151942 Hom.: 25317 Cov.: 32 AF XY: 0.574 AC XY: 42579 AN XY: 74238

African (AFR) AF: 0.457 AC: 18926 AN: 41416

American (AMR) AF: 0.648 AC: 9883 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2133 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3048 AN: 5136

South Asian (SAS) AF: 0.608 AC: 2929 AN: 4818

European-Finnish (FIN) AF: 0.597 AC: 6319 AN: 10582

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41385 AN: 67962

Other (OTH) AF: 0.602 AC: 1269 AN: 2108

Alfa AF: 0.587 Hom.: 5461

Bravo AF: 0.571

Asia WGS AF: 0.596 AC: 2073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.027
DANN	Benign	0.60
PhyloP100		-3.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9332452; hg19: chr9-9393975;