NM_002843.4:c.97-16521C>T

Variant names:

• chr11-48093537-C-T
• rs3942852
• NM_002843.4:c.97-16521C>T

Variant summary

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

The NM_002843.4(PTPRJ):​c.97-16521C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,094 control chromosomes in the GnomAD database, including 39,106 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 0.70 (39106 hom., cov: 32)
• Consequence: PTPRJ NM_002843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 25 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRJ	NM_002843.4	c.97-16521C>T		intron_variant	Intron 1 of 24	ENST00000418331.7	NP_002834.3
PTPRJ	NM_001098503.2	c.97-16521C>T		intron_variant	Intron 1 of 8		NP_001091973.1
PTPRJ	XM_017018085.2	c.49-16521C>T		intron_variant	Intron 1 of 24		XP_016873574.1
PTPRJ	XM_047427374.1	c.439-16521C>T		intron_variant	Intron 1 of 16		XP_047283330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRJ	ENST00000418331.7	c.97-16521C>T		intron_variant	Intron 1 of 24	1	NM_002843.4	ENSP00000400010.2

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106362 AN: 151976 Hom.: 39086 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.700 AC: 106407 AN: 152094 Hom.: 39106 Cov.: 32 AF XY: 0.701 AC XY: 52157 AN XY: 74362

African (AFR) AF: 0.452 AC: 18715 AN: 41432

American (AMR) AF: 0.788 AC: 12044 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2786 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4197 AN: 5178

South Asian (SAS) AF: 0.834 AC: 4027 AN: 4828

European-Finnish (FIN) AF: 0.758 AC: 8019 AN: 10576

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.794 AC: 54010 AN: 68010

Other (OTH) AF: 0.749 AC: 1582 AN: 2112

Alfa AF: 0.749 Hom.: 64687

Bravo AF: 0.691

Asia WGS AF: 0.799 AC: 2774 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.31
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: rs3942852; hg19: chr11-48115089;