rs10758982

Variant names:

• chr9-8533412-A-G
• rs10758982
• NM_002839.4:c.353-4633T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-8533412-A-G
• chr9-8533412-A-T

Variant summary

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

The NM_002839.4(PTPRD):​c.353-4633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,950 control chromosomes in the GnomAD database, including 7,346 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 0.30 (7346 hom., cov: 33)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.353-4633T>C		intron_variant	Intron 14 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.353-4633T>C		intron_variant	Intron 14 of 45	5	NM_002839.4	ENSP00000370593.3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45760 AN: 151830 Hom.: 7314 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.302 AC: 45837 AN: 151950 Hom.: 7346 Cov.: 33 AF XY: 0.300 AC XY: 22281 AN XY: 74272

African (AFR) AF: 0.422 AC: 17497 AN: 41438

American (AMR) AF: 0.257 AC: 3918 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1838 AN: 5152

South Asian (SAS) AF: 0.286 AC: 1382 AN: 4830

European-Finnish (FIN) AF: 0.225 AC: 2381 AN: 10602

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17272 AN: 67924

Other (OTH) AF: 0.260 AC: 548 AN: 2106

Alfa AF: 0.261 Hom.: 9055

Bravo AF: 0.308

Asia WGS AF: 0.323 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		0.18
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: rs10758982; hg19: chr9-8533412;