rs10491912

chr9-9907092-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_002839.4(PTPRD):c.-368+31415C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0318 in 151,916 control chromosomes in the GnomAD database, including 100 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 0.032 (100 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0318 (4829/151916) while in subpopulation NFE AF= 0.0353 (2394/67886). AF 95% confidence interval is 0.0341. There are 100 homozygotes in gnomad4. There are 2406 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd at 4821 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRD	NM_002839.4	c.-368+31415C>G		intron_variant		ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9	c.-368+31415C>G		intron_variant		5	NM_002839.4	P1
PTPRD	ENST00000463477.5	c.-440+31415C>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0318 AC: 4821 AN: 151798 Hom.: 100 Cov.: 32

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.0292

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.0197

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

GnomAD4 genome AF: 0.0318 AC: 4829 AN: 151916 Hom.: 100 Cov.: 32 AF XY: 0.0324 AC XY: 2406 AN XY: 74264

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0168

Gnomad4 ASJ AF: 0.0292

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0353

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0311 Hom.: 7

Bravo AF: 0.0273

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491912; hg19: chr9-9907092;