chr9-9404896-C-A

Variant names:

• chr9-9404896-C-A
• rs10816124
• NM_002839.4:c.-236-7414G>T

Variant summary

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

The NM_002839.4(PTPRD):​c.-236-7414G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,112 control chromosomes in the GnomAD database, including 511 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 0.068 (511 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-236-7414G>T		intron_variant	Intron 8 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-236-7414G>T		intron_variant	Intron 8 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-236-7414G>T		intron_variant	Intron 9 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-236-7414G>T		intron_variant	Intron 10 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10400 AN: 151994 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0599

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0684 AC: 10402 AN: 152112 Hom.: 511 Cov.: 32 AF XY: 0.0654 AC XY: 4867 AN XY: 74380

African (AFR) AF: 0.0182 AC: 756 AN: 41550

American (AMR) AF: 0.0599 AC: 913 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0936 AC: 325 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4820

European-Finnish (FIN) AF: 0.0719 AC: 762 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7383 AN: 67936

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0927 Hom.: 1331

Bravo AF: 0.0640

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-0.44
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: rs10816124; hg19: chr9-9404896;