NM_002839.4:c.-367-34904C>T

Variant names:

• chr9-9801755-G-A
• rs1613507
• NM_002839.4:c.-367-34904C>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.-367-34904C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,800 control chromosomes in the GnomAD database, including 33,177 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 0.64 (33177 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773
• 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]

ENSG00000230920 (HGNC:):

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 = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-367-34904C>T		intron_variant	Intron 5 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-367-34904C>T		intron_variant	Intron 5 of 45	5	NM_002839.4	ENSP00000370593.3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97184 AN: 151682 Hom.: 33109 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.641 AC: 97313 AN: 151800 Hom.: 33177 Cov.: 32 AF XY: 0.643 AC XY: 47703 AN XY: 74198

African (AFR) AF: 0.871 AC: 36144 AN: 41476

American (AMR) AF: 0.660 AC: 10062 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1656 AN: 3460

East Asian (EAS) AF: 0.871 AC: 4494 AN: 5158

South Asian (SAS) AF: 0.535 AC: 2577 AN: 4820

European-Finnish (FIN) AF: 0.543 AC: 5704 AN: 10512

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34667 AN: 67826

Other (OTH) AF: 0.595 AC: 1254 AN: 2106

Alfa AF: 0.558 Hom.: 17817

Bravo AF: 0.665

Asia WGS AF: 0.745 AC: 2590 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	3.2
DANN	Benign	0.44
PhyloP100		0.77
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: rs1613507; hg19: chr9-9801755;