rs1975197

Variant names:

• chr9-8846955-G-A
• rs1975197
• NM_002839.4:c.-103-113009C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-8846955-G-A
• chr9-8846955-G-C
• chr9-8846955-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.-103-113009C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,970 control chromosomes in the GnomAD database, including 2,187 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 0.16 (2187 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 49 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 (EAS) allele frequency at 95% confidence interval = 0.3 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	NM_002839.4	MANE Select	c.-103-113009C>T		intron	N/A	NP_002830.1
	PTPRD	NM_001377958.1		c.-104+10683C>T		intron	N/A	NP_001364887.1
	PTPRD	NM_001378058.1		c.-104+10683C>T		intron	N/A	NP_001364987.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRD	ENST00000381196.9	TSL:5 MANE Select	c.-103-113009C>T		intron	N/A	ENSP00000370593.3
	PTPRD	ENST00000463477.5	TSL:1	c.-103-113009C>T		intron	N/A	ENSP00000417661.1
	PTPRD	ENST00000850942.1		c.-103-113009C>T		intron	N/A	ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24446 AN: 151852 Hom.: 2188 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0892

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.161 AC: 24466 AN: 151970 Hom.: 2187 Cov.: 32 AF XY: 0.162 AC XY: 12022 AN XY: 74278

African (AFR) AF: 0.115 AC: 4784 AN: 41452

American (AMR) AF: 0.222 AC: 3387 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0892 AC: 309 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1610 AN: 5144

South Asian (SAS) AF: 0.233 AC: 1116 AN: 4796

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10570

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11647 AN: 67964

Other (OTH) AF: 0.164 AC: 345 AN: 2106

Alfa AF: 0.170 Hom.: 10364

Bravo AF: 0.167

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		0.21
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: rs1975197; hg19: chr9-8846955;