NM_002839.4:c.3413+1711A>G

Variant names:

• chr9-8482408-T-C
• rs10117986
• NM_002839.4:c.3413+1711A>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.3413+1711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,612 control chromosomes in the GnomAD database, including 8,240 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 0.33 (8240 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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.3413+1711A>G		intron	N/A	NP_002830.1
	PTPRD	NM_001377958.1		c.3416+1711A>G		intron	N/A	NP_001364887.1
	PTPRD	NM_001378058.1		c.3413+1711A>G		intron	N/A	NP_001364987.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.3413+1711A>G		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000355233.9	TSL:1	c.2180+1711A>G		intron	N/A	ENSP00000347373.5
	PTPRD	ENST00000397606.7	TSL:1	c.2150+1711A>G		intron	N/A	ENSP00000380731.3

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49432 AN: 151494 Hom.: 8215 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.327 AC: 49513 AN: 151612 Hom.: 8240 Cov.: 31 AF XY: 0.325 AC XY: 24045 AN XY: 74048

African (AFR) AF: 0.407 AC: 16809 AN: 41280

American (AMR) AF: 0.315 AC: 4797 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3464

East Asian (EAS) AF: 0.359 AC: 1827 AN: 5086

South Asian (SAS) AF: 0.259 AC: 1246 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2925 AN: 10494

Middle Eastern (MID) AF: 0.276 AC: 80 AN: 290

European-Non Finnish (NFE) AF: 0.297 AC: 20199 AN: 67950

Other (OTH) AF: 0.292 AC: 616 AN: 2106

Alfa AF: 0.293 Hom.: 11191

Bravo AF: 0.332

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.43
PhyloP100		-2.0
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: rs10117986; hg19: chr9-8482408;