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GeneBe

rs1893217

Variant summary

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

The NM_002828.4(PTPN2):c.858+4862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,242 control chromosomes in the GnomAD database, including 1,411 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 0.12 ( 1411 hom., cov: 32)

Consequence

PTPN2
NM_002828.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.647
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=-0.77).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPN2NM_002828.4 linkuse as main transcriptc.858+4862T>C intron_variant ENST00000309660.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPN2ENST00000309660.10 linkuse as main transcriptc.858+4862T>C intron_variant 1 NM_002828.4 A1P17706-1

Frequencies

GnomAD3 genomes
AF:
0.125
AC:
18947
AN:
152124
Hom.:
1410
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0580
Gnomad AMI
AF:
0.0461
Gnomad AMR
AF:
0.0966
Gnomad ASJ
AF:
0.0969
Gnomad EAS
AF:
0.171
Gnomad SAS
AF:
0.189
Gnomad FIN
AF:
0.151
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.162
Gnomad OTH
AF:
0.117
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.124
AC:
18946
AN:
152242
Hom.:
1411
Cov.:
32
AF XY:
0.126
AC XY:
9389
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0579
Gnomad4 AMR
AF:
0.0965
Gnomad4 ASJ
AF:
0.0969
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.189
Gnomad4 FIN
AF:
0.151
Gnomad4 NFE
AF:
0.162
Gnomad4 OTH
AF:
0.115
Alfa
AF:
0.152
Hom.:
4277
Bravo
AF:
0.116
Asia WGS
AF:
0.177
AC:
616
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
Cadd
Benign
1.0
Dann
Benign
0.86

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: rs1893217; hg19: chr18-12809340; API