18-12857759-G-A

Variant summary

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

The ENST00000309660.10(PTPN2):​c.160+1405C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0299 in 152,120 control chromosomes in the GnomAD database, including 100 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 0.030 ( 100 hom., cov: 32)

Consequence

PTPN2
ENST00000309660.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510
Variant links:
Genes affected
PTPN2 (HGNC:9650): (protein tyrosine phosphatase non-receptor type 2) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. Members of the PTP family share a highly conserved catalytic motif, which is essential for the catalytic activity. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. Epidermal growth factor receptor and the adaptor protein Shc were reported to be substrates of this PTP, which suggested the roles in growth factor mediated cell signaling. Multiple alternatively spliced transcript variants encoding different isoforms have been found. Two highly related but distinctly processed pseudogenes that localize to chromosomes 1 and 13, respectively, have been reported. [provided by RefSeq, May 2011]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0907 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTPN2NM_002828.4 linkuse as main transcriptc.160+1405C>T intron_variant ENST00000309660.10 NP_002819.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTPN2ENST00000309660.10 linkuse as main transcriptc.160+1405C>T intron_variant 1 NM_002828.4 ENSP00000311857 A1P17706-1

Frequencies

GnomAD3 genomes
AF:
0.0299
AC:
4548
AN:
152002
Hom.:
101
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00771
Gnomad AMI
AF:
0.00659
Gnomad AMR
AF:
0.0205
Gnomad ASJ
AF:
0.0409
Gnomad EAS
AF:
0.0166
Gnomad SAS
AF:
0.0985
Gnomad FIN
AF:
0.0300
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0416
Gnomad OTH
AF:
0.0263
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0299
AC:
4545
AN:
152120
Hom.:
100
Cov.:
32
AF XY:
0.0306
AC XY:
2274
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.00769
Gnomad4 AMR
AF:
0.0205
Gnomad4 ASJ
AF:
0.0409
Gnomad4 EAS
AF:
0.0168
Gnomad4 SAS
AF:
0.0980
Gnomad4 FIN
AF:
0.0300
Gnomad4 NFE
AF:
0.0416
Gnomad4 OTH
AF:
0.0260
Alfa
AF:
0.0381
Hom.:
20
Bravo
AF:
0.0257
Asia WGS
AF:
0.0690
AC:
239
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.9
DANN
Benign
0.57

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: rs62097857; hg19: chr18-12857758; API