chr9-8682672-A-G

Variant names:

• chr9-8682672-A-G
• rs10511506
• NM_002839.4:c.65-45828T>C

Variant summary

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

The NM_002839.4(PTPRD):​c.65-45828T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,230 control chromosomes in the GnomAD database, including 1,041 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 0.10 (1041 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.65-45828T>C		intron_variant	Intron 12 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.65-45828T>C		intron_variant	Intron 12 of 45	5	NM_002839.4	ENSP00000370593.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15827 AN: 152112 Hom.: 1043 Cov.: 32

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.104 AC: 15826 AN: 152230 Hom.: 1041 Cov.: 32 AF XY: 0.107 AC XY: 7998 AN XY: 74452

African (AFR) AF: 0.0328 AC: 1364 AN: 41558

American (AMR) AF: 0.0965 AC: 1476 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 331 AN: 3464

East Asian (EAS) AF: 0.0488 AC: 253 AN: 5182

South Asian (SAS) AF: 0.155 AC: 748 AN: 4830

European-Finnish (FIN) AF: 0.196 AC: 2079 AN: 10582

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9169 AN: 67998

Other (OTH) AF: 0.110 AC: 232 AN: 2116

Alfa AF: 0.125 Hom.: 2335

Bravo AF: 0.0916

Asia WGS AF: 0.100 AC: 346 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.89
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: rs10511506; hg19: chr9-8682672;