rs3741410

Positions:

• chr11-48147112-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002843.4(PTPRJ):​c.2999+149T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 717,440 control chromosomes in the GnomAD database, including 9,918 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 0.19 (3178 hom., cov: 32)
  • Exomes 𝑓: 0.15 (6740 hom.)
• Consequence: PTPRJ NM_002843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPRJ	NM_002843.4	c.2999+149T>G		intron_variant		ENST00000418331.7	NP_002834.3
PTPRJ	XM_017018085.2	c.2951+149T>G		intron_variant			XP_016873574.1
PTPRJ	XM_047427374.1	c.3253+1988T>G		intron_variant			XP_047283330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPRJ	ENST00000418331.7	c.2999+149T>G		intron_variant		1	NM_002843.4	ENSP00000400010.2
PTPRJ	ENST00000698881.1	c.3341+149T>G		intron_variant				ENSP00000514003.1
PTPRJ	ENST00000527026.1	n.135+149T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28772 AN: 152060 Hom.: 3174 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.147 AC: 83072 AN: 565262 Hom.: 6740 AF XY: 0.146 AC XY: 43976 AN XY: 300506

Gnomad4 AFR exome AF: 0.303

Gnomad4 AMR exome AF: 0.135

Gnomad4 ASJ exome AF: 0.123

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.144

Gnomad4 FIN exome AF: 0.176

Gnomad4 NFE exome AF: 0.138

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.189 AC: 28800 AN: 152178 Hom.: 3178 Cov.: 32 AF XY: 0.191 AC XY: 14190 AN XY: 74410

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.150

Alfa AF: 0.150 Hom.: 1151

Bravo AF: 0.190

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.087
DANN	Benign	0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs3741410; hg19: chr11-48168664;