rs294856

Variant names:

• chr9-10192290-A-C
• rs294856
• NM_002839.4:c.-545+148673T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-10192290-A-C
• chr9-10192290-A-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.-545+148673T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,596 control chromosomes in the GnomAD database, including 24,832 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 0.54 (24832 hom., cov: 29)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	NM_002839.4	MANE Select	c.-545+148673T>G		intron	N/A	NP_002830.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.-545+148673T>G		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000463477.5	TSL:1	c.-617+148673T>G		intron	N/A	ENSP00000417661.1
	PTPRD	ENST00000850942.1		c.-634+7132T>G		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82281 AN: 151478 Hom.: 24789 Cov.: 29

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.543 AC: 82386 AN: 151596 Hom.: 24832 Cov.: 29 AF XY: 0.541 AC XY: 40062 AN XY: 74022

African (AFR) AF: 0.821 AC: 33938 AN: 41338

American (AMR) AF: 0.413 AC: 6272 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2879 AN: 5144

South Asian (SAS) AF: 0.506 AC: 2433 AN: 4808

European-Finnish (FIN) AF: 0.445 AC: 4669 AN: 10492

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29061 AN: 67852

Other (OTH) AF: 0.517 AC: 1086 AN: 2102

Alfa AF: 0.461 Hom.: 75165

Bravo AF: 0.552

Asia WGS AF: 0.544 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.47
DANN	Benign	0.46
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs294856; hg19: chr9-10192290;