rs968079

Variant names:

• chr9-9173304-G-A
• rs968079
• NM_002839.4:c.-143+10000C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-9173304-G-A
• chr9-9173304-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.-143+10000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,050 control chromosomes in the GnomAD database, including 46,965 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 0.77 (46965 hom., cov: 32)
• Consequence: PTPRD NM_002839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRD	NM_002839.4	c.-143+10000C>T		intron_variant	Intron 10 of 45	ENST00000381196.9	NP_002830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRD	ENST00000381196.9	c.-143+10000C>T		intron_variant	Intron 10 of 45	5	NM_002839.4	ENSP00000370593.3
PTPRD	ENST00000463477.5	c.-143+10000C>T		intron_variant	Intron 11 of 16	1		ENSP00000417661.1
PTPRD	ENST00000850942.1	c.-143+10000C>T		intron_variant	Intron 12 of 47			ENSP00000521027.1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116899 AN: 151932 Hom.: 46959 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.769 AC: 116949 AN: 152050 Hom.: 46965 Cov.: 32 AF XY: 0.769 AC XY: 57148 AN XY: 74306

African (AFR) AF: 0.515 AC: 21347 AN: 41438

American (AMR) AF: 0.845 AC: 12906 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2980 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3506 AN: 5150

South Asian (SAS) AF: 0.941 AC: 4539 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8656 AN: 10574

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60181 AN: 68008

Other (OTH) AF: 0.815 AC: 1722 AN: 2112

Alfa AF: 0.850 Hom.: 95813

Bravo AF: 0.755

Asia WGS AF: 0.778 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.58
PhyloP100		-0.11
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: rs968079; hg19: chr9-9173304;