9-9181361-G-T

Variant names:

• chr9-9181361-G-T
• rs1889820
• NM_002839.4:c.-143+1943C>A

Variant summary

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

The ENST00000381196.9(PTPRD):​c.-143+1943C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,566 control chromosomes in the GnomAD database, including 33,032 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 0.66 (33032 hom., cov: 30)
• Consequence: PTPRD ENST00000381196.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000381196.9. 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.-143+1943C>A		intron	N/A	NP_002830.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.-143+1943C>A		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000463477.5	TSL:1	c.-143+1943C>A		intron	N/A	ENSP00000417661.1
	PTPRD	ENST00000850942.1		c.-143+1943C>A		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99323 AN: 151446 Hom.: 32995 Cov.: 30

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.656 AC: 99415 AN: 151566 Hom.: 33032 Cov.: 30 AF XY: 0.657 AC XY: 48656 AN XY: 74010

African (AFR) AF: 0.572 AC: 23631 AN: 41318

American (AMR) AF: 0.718 AC: 10888 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3584 AN: 5140

South Asian (SAS) AF: 0.843 AC: 4056 AN: 4814

European-Finnish (FIN) AF: 0.651 AC: 6831 AN: 10496

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46209 AN: 67864

Other (OTH) AF: 0.643 AC: 1349 AN: 2098

Alfa AF: 0.665 Hom.: 55054

Bravo AF: 0.654

Asia WGS AF: 0.758 AC: 2630 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.39
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: rs1889820; hg19: chr9-9181361;