9-9588336-A-G

Variant names:

• chr9-9588336-A-G
• rs610789
• NM_002839.4:c.-286-13555T>C

Variant summary

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

The NM_002839.4(PTPRD):​c.-286-13555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,652 control chromosomes in the GnomAD database, including 7,908 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 0.31 (7908 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-286-13555T>C		intron_variant	Intron 7 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-286-13555T>C		intron_variant	Intron 7 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-358-13555T>C		intron_variant	Intron 7 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-286-13555T>C		intron_variant	Intron 9 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47578 AN: 151534 Hom.: 7906 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.314 AC: 47602 AN: 151652 Hom.: 7908 Cov.: 31 AF XY: 0.311 AC XY: 23068 AN XY: 74106

African (AFR) AF: 0.262 AC: 10833 AN: 41394

American (AMR) AF: 0.252 AC: 3832 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3466

East Asian (EAS) AF: 0.182 AC: 935 AN: 5128

South Asian (SAS) AF: 0.152 AC: 731 AN: 4810

European-Finnish (FIN) AF: 0.408 AC: 4307 AN: 10560

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24826 AN: 67802

Other (OTH) AF: 0.316 AC: 666 AN: 2108

Alfa AF: 0.343 Hom.: 39676

Bravo AF: 0.301

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		-0.38
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: rs610789; hg19: chr9-9588336;