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. Variant got -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

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

Verdict is Benign. Variant got -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
PTPRD	ENST00000463477.5	c.-439-34904C>T		intron_variant	Intron 5 of 16	1		ENSP00000417661.1
ENSG00000230920	ENST00000449531.1	n.315+1081G>A		intron_variant	Intron 2 of 2	2

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

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.595

Alfa AF: 0.541 Hom.: 11503

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1613507; hg19: chr9-9801755;