rs1544056

chr9-10279606-C-Achr9-10279606-C-Gchr9-10279606-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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/exons	MANE	UniProt
PTPRD	NM_002839.4	c.-545+61357G>T		intron_variant		ENST00000381196.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRD	ENST00000381196.9	c.-545+61357G>T		intron_variant		5	NM_002839.4	P1
PTPRD	ENST00000463477.5	c.-617+61357G>T		intron_variant		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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.320

Alfa AF: 0.240 Hom.: 2726

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544056; hg19: chr9-10279606;