chr9-8351957-G-A

Variant names:

• chr9-8351957-G-A
• rs3847291
• NM_002839.4:c.4662-9979C>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.4662-9979C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,670 control chromosomes in the GnomAD database, including 3,786 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 0.20 (3786 hom., cov: 29)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 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.4662-9979C>T		intron	N/A	NP_002830.1
	PTPRD	NM_001377958.1		c.4722-9979C>T		intron	N/A	NP_001364887.1
	PTPRD	NM_001378058.1		c.4677-9979C>T		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.4662-9979C>T		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000355233.9	TSL:1	c.3444-9979C>T		intron	N/A	ENSP00000347373.5
	PTPRD	ENST00000397606.7	TSL:1	c.3441-9979C>T		intron	N/A	ENSP00000380731.3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 29977 AN: 151556 Hom.: 3780 Cov.: 29

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.198 AC: 30007 AN: 151670 Hom.: 3786 Cov.: 29 AF XY: 0.205 AC XY: 15156 AN XY: 74104

African (AFR) AF: 0.274 AC: 11324 AN: 41300

American (AMR) AF: 0.351 AC: 5342 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3464

East Asian (EAS) AF: 0.349 AC: 1788 AN: 5122

South Asian (SAS) AF: 0.207 AC: 993 AN: 4800

European-Finnish (FIN) AF: 0.152 AC: 1595 AN: 10506

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8099 AN: 67958

Other (OTH) AF: 0.169 AC: 356 AN: 2102

Alfa AF: 0.131 Hom.: 1303

Bravo AF: 0.219

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.31
PhyloP100		0.31
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: rs3847291; hg19: chr9-8351957; COSMIC: COSV61976906;