NM_002839.4:c.-545+93310A>G

Variant names:

• chr9-10247653-T-C
• rs4741021
• NM_002839.4:c.-545+93310A>G

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+93310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,938 control chromosomes in the GnomAD database, including 24,792 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 0.55 (24792 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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.-545+93310A>G		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.-545+93310A>G		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000463477.5	TSL:1	c.-617+93310A>G		intron	N/A	ENSP00000417661.1
	PTPRD	ENST00000850942.1		c.-705-48160A>G		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83795 AN: 151820 Hom.: 24794 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.552 AC: 83821 AN: 151938 Hom.: 24792 Cov.: 31 AF XY: 0.554 AC XY: 41142 AN XY: 74250

African (AFR) AF: 0.326 AC: 13522 AN: 41446

American (AMR) AF: 0.547 AC: 8346 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2051 AN: 3466

East Asian (EAS) AF: 0.729 AC: 3762 AN: 5164

South Asian (SAS) AF: 0.601 AC: 2899 AN: 4820

European-Finnish (FIN) AF: 0.652 AC: 6866 AN: 10532

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44389 AN: 67940

Other (OTH) AF: 0.551 AC: 1162 AN: 2110

Alfa AF: 0.582 Hom.: 3467

Bravo AF: 0.534

Asia WGS AF: 0.610 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		-0.065
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: rs4741021; hg19: chr9-10247653;