9-8868177-T-C

Variant names:

• chr9-8868177-T-C
• rs2217711
• NM_002839.4:c.-103-134231A>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.-103-134231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,014 control chromosomes in the GnomAD database, including 54,482 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 0.85 (54482 hom., cov: 30)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 13 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-103-134231A>G		intron_variant	Intron 11 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-103-134231A>G		intron_variant	Intron 11 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-103-134231A>G		intron_variant	Intron 12 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-103-134231A>G		intron_variant	Intron 13 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128502 AN: 151896 Hom.: 54422 Cov.: 30

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.846 AC: 128620 AN: 152014 Hom.: 54482 Cov.: 30 AF XY: 0.849 AC XY: 63083 AN XY: 74334

African (AFR) AF: 0.840 AC: 34816 AN: 41466

American (AMR) AF: 0.864 AC: 13172 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3058 AN: 3466

East Asian (EAS) AF: 0.975 AC: 5026 AN: 5156

South Asian (SAS) AF: 0.901 AC: 4345 AN: 4822

European-Finnish (FIN) AF: 0.837 AC: 8843 AN: 10570

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56520 AN: 67970

Other (OTH) AF: 0.872 AC: 1844 AN: 2114

Alfa AF: 0.841 Hom.: 82093

Bravo AF: 0.851

Asia WGS AF: 0.932 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.36
PhyloP100		-0.032
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: rs2217711; hg19: chr9-8868177;