rs10977624

Variant names:

• chr9-9270120-G-C
• rs10977624
• NM_002839.4:c.-202-86757C>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.-202-86757C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,000 control chromosomes in the GnomAD database, including 1,140 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 (1140 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-202-86757C>G		intron_variant	Intron 9 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-202-86757C>G		intron_variant	Intron 9 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-202-86757C>G		intron_variant	Intron 10 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-202-86757C>G		intron_variant	Intron 11 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15332 AN: 150892 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.0271

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.000589

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.102 AC: 15328 AN: 151000 Hom.: 1140 Cov.: 32 AF XY: 0.0969 AC XY: 7146 AN XY: 73758

African (AFR) AF: 0.0270 AC: 1117 AN: 41332

American (AMR) AF: 0.0911 AC: 1376 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 348 AN: 3450

East Asian (EAS) AF: 0.000590 AC: 3 AN: 5084

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1239 AN: 10470

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10882 AN: 67442

Other (OTH) AF: 0.0900 AC: 188 AN: 2090

Alfa AF: 0.132 Hom.: 239

Bravo AF: 0.0957

Asia WGS AF: 0.0150 AC: 52 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.72
PhyloP100		-1.1
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: rs10977624; hg19: chr9-9270120; COSMIC: COSV67005927;