chr9-8366629-G-C

Variant names:

• chr9-8366629-G-C
• rs10115782
• NM_002839.4:c.4661+9307C>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.4661+9307C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,216 control chromosomes in the GnomAD database, including 644 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 0.089 (644 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0983 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.4661+9307C>G		intron	N/A	NP_002830.1	P23468-1
	PTPRD	NM_001377958.1		c.4721+9307C>G		intron	N/A	NP_001364887.1
	PTPRD	NM_001378058.1		c.4676+9307C>G		intron	N/A	NP_001364987.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.4661+9307C>G		intron	N/A	ENSP00000370593.3	P23468-1
	PTPRD	ENST00000355233.9	TSL:1	c.3443+9307C>G		intron	N/A	ENSP00000347373.5	P23468-6
	PTPRD	ENST00000397606.7	TSL:1	c.3440+9307C>G		intron	N/A	ENSP00000380731.3	P23468-4

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13478 AN: 152098 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.0921

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

GnomAD4 genome AF: 0.0886 AC: 13491 AN: 152216 Hom.: 644 Cov.: 32 AF XY: 0.0858 AC XY: 6387 AN XY: 74436

African (AFR) AF: 0.101 AC: 4187 AN: 41524

American (AMR) AF: 0.0658 AC: 1006 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 571 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5188

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4824

European-Finnish (FIN) AF: 0.0587 AC: 622 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6248 AN: 68018

Other (OTH) AF: 0.0912 AC: 192 AN: 2106

Alfa AF: 0.0211 Hom.: 11

Bravo AF: 0.0907

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.69
PhyloP100		-0.73
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: rs10115782; hg19: chr9-8366629;