9-10167292-G-C

Variant names:

• chr9-10167292-G-C
• rs10958932
• NM_002839.4:c.-544-133502C>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.-544-133502C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,680 control chromosomes in the GnomAD database, including 12,503 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 0.39 (12503 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002839.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	NM_002839.4	MANE Select	c.-544-133502C>G		intron	N/A	NP_002830.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.-544-133502C>G		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000463477.5	TSL:1	c.-616-133502C>G		intron	N/A	ENSP00000417661.1
	PTPRD	ENST00000850942.1		c.-634+32130C>G		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59563 AN: 151562 Hom.: 12468 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.393 AC: 59671 AN: 151680 Hom.: 12503 Cov.: 31 AF XY: 0.393 AC XY: 29106 AN XY: 74114

African (AFR) AF: 0.550 AC: 22732 AN: 41350

American (AMR) AF: 0.344 AC: 5247 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1329 AN: 3462

East Asian (EAS) AF: 0.296 AC: 1522 AN: 5144

South Asian (SAS) AF: 0.420 AC: 2019 AN: 4810

European-Finnish (FIN) AF: 0.348 AC: 3666 AN: 10528

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21952 AN: 67826

Other (OTH) AF: 0.384 AC: 809 AN: 2108

Alfa AF: 0.183 Hom.: 320

Bravo AF: 0.399

Asia WGS AF: 0.374 AC: 1302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.019
DANN	Benign	0.43
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10958932; hg19: chr9-10167292;