chr9-10279606-C-A

Variant names:

• chr9-10279606-C-A
• rs1544056
• NM_002839.4:c.-545+61357G>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.-545+61357G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,682 control chromosomes in the GnomAD database, including 12,606 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 0.36 (12606 hom., cov: 31)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-545+61357G>T		intron_variant	Intron 3 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-545+61357G>T		intron_variant	Intron 3 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-617+61357G>T		intron_variant	Intron 3 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-706+61357G>T		intron_variant	Intron 3 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54486 AN: 151564 Hom.: 12566 Cov.: 31

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.360 AC: 54600 AN: 151682 Hom.: 12606 Cov.: 31 AF XY: 0.364 AC XY: 26957 AN XY: 74104

African (AFR) AF: 0.630 AC: 26041 AN: 41328

American (AMR) AF: 0.422 AC: 6431 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 687 AN: 3456

East Asian (EAS) AF: 0.391 AC: 2007 AN: 5138

South Asian (SAS) AF: 0.499 AC: 2394 AN: 4794

European-Finnish (FIN) AF: 0.203 AC: 2135 AN: 10522

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14122 AN: 67906

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.266 Hom.: 13897

Bravo AF: 0.384

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.0050
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1544056; hg19: chr9-10279606;