chr11-48069751-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002843.4(PTPRJ):​c.97-40307T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,106 control chromosomes in the GnomAD database, including 28,526 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 0.57 ( 28526 hom., cov: 32)

Consequence

PTPRJ
NM_002843.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPRJNM_002843.4 linkuse as main transcriptc.97-40307T>G intron_variant ENST00000418331.7
PTPRJNM_001098503.2 linkuse as main transcriptc.97-40307T>G intron_variant
PTPRJXM_017018085.2 linkuse as main transcriptc.49-40307T>G intron_variant
PTPRJXM_047427374.1 linkuse as main transcriptc.439-40307T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPRJENST00000418331.7 linkuse as main transcriptc.97-40307T>G intron_variant 1 NM_002843.4 P2Q12913-1

Frequencies

GnomAD3 genomes
AF:
0.571
AC:
86733
AN:
151988
Hom.:
28515
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.864
Gnomad AMR
AF:
0.688
Gnomad ASJ
AF:
0.698
Gnomad EAS
AF:
0.805
Gnomad SAS
AF:
0.771
Gnomad FIN
AF:
0.710
Gnomad MID
AF:
0.639
Gnomad NFE
AF:
0.692
Gnomad OTH
AF:
0.621
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.570
AC:
86761
AN:
152106
Hom.:
28526
Cov.:
32
AF XY:
0.577
AC XY:
42890
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.220
Gnomad4 AMR
AF:
0.688
Gnomad4 ASJ
AF:
0.698
Gnomad4 EAS
AF:
0.806
Gnomad4 SAS
AF:
0.770
Gnomad4 FIN
AF:
0.710
Gnomad4 NFE
AF:
0.692
Gnomad4 OTH
AF:
0.627
Alfa
AF:
0.616
Hom.:
4065
Bravo
AF:
0.556
Asia WGS
AF:
0.758
AC:
2637
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
5.6
DANN
Benign
0.84

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10838798; hg19: chr11-48091303; API