11-47996803-A-G

Variant names:

• chr11-47996803-A-G
• rs4752805
• NM_002843.4:c.96+15795A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002843.4(PTPRJ):​c.96+15795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,184 control chromosomes in the GnomAD database, including 18,132 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 0.41 (18132 hom., cov: 32)
• Consequence: PTPRJ NM_002843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 18 publications found

Genes affected

PTPRJ (HGNC:9673): (protein tyrosine phosphatase receptor type J) 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 possesses an extracellular region containing five fibronectin type III repeats, a single transmembrane region, and a single intracytoplasmic catalytic domain, and thus represents a receptor-type PTP. This protein is present in all hematopoietic lineages, and was shown to negatively regulate T cell receptor signaling possibly through interfering with the phosphorylation of Phospholipase C Gamma 1 and Linker for Activation of T Cells. This protein can also dephosphorylate the PDGF beta receptor, and may be involved in UV-induced signal transduction. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

PTPRJ Gene-Disease associations (from GenCC):

• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• thrombocytopenia 10

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• colorectal cancer

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002843.4. 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
	PTPRJ	NM_002843.4	MANE Select	c.96+15795A>G		intron	N/A	NP_002834.3
	PTPRJ	NM_001098503.2		c.96+15795A>G		intron	N/A	NP_001091973.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPRJ	ENST00000418331.7	TSL:1 MANE Select	c.96+15795A>G		intron	N/A	ENSP00000400010.2
	PTPRJ	ENST00000440289.6	TSL:1	c.96+15795A>G		intron	N/A	ENSP00000409733.2
	PTPRJ	ENST00000698881.1		c.438+15795A>G		intron	N/A	ENSP00000514003.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62695 AN: 152066 Hom.: 18082 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.413 AC: 62796 AN: 152184 Hom.: 18132 Cov.: 32 AF XY: 0.408 AC XY: 30373 AN XY: 74398

African (AFR) AF: 0.828 AC: 34387 AN: 41522

American (AMR) AF: 0.272 AC: 4162 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1181 AN: 5174

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4822

European-Finnish (FIN) AF: 0.283 AC: 2999 AN: 10588

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17132 AN: 67998

Other (OTH) AF: 0.342 AC: 722 AN: 2114

Alfa AF: 0.298 Hom.: 15982

Bravo AF: 0.429

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.083
DANN	Benign	0.27
PhyloP100		-1.3
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: rs4752805; hg19: chr11-48018355;