rs10977017

Variant names:

• chr9-8380546-G-A
• rs10977017
• NM_002839.4:c.4387-3820C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-8380546-G-A
• chr9-8380546-G-C
• chr9-8380546-G-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.4387-3820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,054 control chromosomes in the GnomAD database, including 7,262 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 0.28 (7262 hom., cov: 33)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002839.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	NM_002839.4	MANE Select	c.4387-3820C>T		intron	N/A	NP_002830.1
	PTPRD	NM_001377958.1		c.4447-3820C>T		intron	N/A	NP_001364887.1
	PTPRD	NM_001378058.1		c.4402-3820C>T		intron	N/A	NP_001364987.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.4387-3820C>T		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000355233.9	TSL:1	c.3169-3820C>T		intron	N/A	ENSP00000347373.5
	PTPRD	ENST00000397606.7	TSL:1	c.3166-3820C>T		intron	N/A	ENSP00000380731.3

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42856 AN: 151934 Hom.: 7232 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.282 AC: 42930 AN: 152054 Hom.: 7262 Cov.: 33 AF XY: 0.288 AC XY: 21431 AN XY: 74330

African (AFR) AF: 0.409 AC: 16978 AN: 41468

American (AMR) AF: 0.366 AC: 5586 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2834 AN: 5176

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4820

European-Finnish (FIN) AF: 0.186 AC: 1962 AN: 10546

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12154 AN: 67988

Other (OTH) AF: 0.257 AC: 543 AN: 2110

Alfa AF: 0.221 Hom.: 895

Bravo AF: 0.301

Asia WGS AF: 0.483 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.63
DANN	Benign	0.81
PhyloP100		-0.36
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: rs10977017; hg19: chr9-8380546;