chr9-9802058-G-A

Variant names:

• chr9-9802058-G-A
• rs1408126
• NM_002839.4:c.-367-35207C>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.-367-35207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,910 control chromosomes in the GnomAD database, including 33,273 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 (33273 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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.-367-35207C>T		intron	N/A	NP_002830.1
	LOC105375972	NR_135135.1		n.346+1384G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.-367-35207C>T		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000463477.5	TSL:1	c.-439-35207C>T		intron	N/A	ENSP00000417661.1
	PTPRD	ENST00000850942.1		c.-367-35207C>T		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97371 AN: 151792 Hom.: 33204 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.642 AC: 97501 AN: 151910 Hom.: 33273 Cov.: 32 AF XY: 0.644 AC XY: 47789 AN XY: 74224

African (AFR) AF: 0.870 AC: 36149 AN: 41532

American (AMR) AF: 0.662 AC: 10108 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3466

East Asian (EAS) AF: 0.873 AC: 4513 AN: 5170

South Asian (SAS) AF: 0.536 AC: 2577 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5742 AN: 10556

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34743 AN: 67806

Other (OTH) AF: 0.598 AC: 1258 AN: 2104

Alfa AF: 0.552 Hom.: 13260

Bravo AF: 0.666

Asia WGS AF: 0.743 AC: 2584 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.57
PhyloP100		-0.20
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: rs1408126; hg19: chr9-9802058;