rs10511549

Variant names:

• chr9-10548235-G-C
• rs10511549
• NM_002839.4:c.-600+64163C>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.-600+64163C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,054 control chromosomes in the GnomAD database, including 4,810 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 0.23 (4810 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 3 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 = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-600+64163C>G		intron_variant	Intron 2 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-600+64163C>G		intron_variant	Intron 2 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-672+64163C>G		intron_variant	Intron 2 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-761+64163C>G		intron_variant	Intron 2 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35204 AN: 151936 Hom.: 4811 Cov.: 32

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.231 AC: 35196 AN: 152054 Hom.: 4810 Cov.: 32 AF XY: 0.233 AC XY: 17346 AN XY: 74326

African (AFR) AF: 0.0800 AC: 3319 AN: 41504

American (AMR) AF: 0.220 AC: 3361 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1292 AN: 5170

South Asian (SAS) AF: 0.277 AC: 1333 AN: 4812

European-Finnish (FIN) AF: 0.306 AC: 3228 AN: 10558

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20832 AN: 67946

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.263 Hom.: 750

Bravo AF: 0.216

Asia WGS AF: 0.219 AC: 759 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	1.1
DANN	Benign	0.41
PhyloP100		-0.043
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: rs10511549; hg19: chr9-10548235;