NM_002839.4:c.-103-31097T>C

Variant names:

• chr9-8765043-A-G
• rs7874851
• NM_002839.4:c.-103-31097T>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.-103-31097T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,162 control chromosomes in the GnomAD database, including 565 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 0.054 (565 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-103-31097T>C		intron_variant	Intron 11 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-103-31097T>C		intron_variant	Intron 11 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-103-31097T>C		intron_variant	Intron 12 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-103-31097T>C		intron_variant	Intron 13 of 47			ENSP00000521027.1
PTPRD	ENST00000481079.1	c.-103-31097T>C		intron_variant	Intron 1 of 3	2		ENSP00000417890.1

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8200 AN: 152046 Hom.: 556 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0203

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0255

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.00868

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0542 AC: 8249 AN: 152162 Hom.: 565 Cov.: 31 AF XY: 0.0531 AC XY: 3951 AN XY: 74380

African (AFR) AF: 0.162 AC: 6723 AN: 41488

American (AMR) AF: 0.0203 AC: 310 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3468

East Asian (EAS) AF: 0.0254 AC: 131 AN: 5164

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4818

European-Finnish (FIN) AF: 0.00868 AC: 92 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0113 AC: 767 AN: 68026

Other (OTH) AF: 0.0369 AC: 78 AN: 2114

Alfa AF: 0.0385 Hom.: 43

Bravo AF: 0.0596

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.41
Mutation Taster		=99/1	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: rs7874851; hg19: chr9-8765043;