chr18-12831024-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002828.4(PTPN2):c.279A>G(p.Thr93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000277 in 1,607,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00029 ( 0 hom. )
Consequence
PTPN2
NM_002828.4 synonymous
NM_002828.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.695
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 18-12831024-T-C is Benign according to our data. Variant chr18-12831024-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 743145.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.695 with no splicing effect.
BS2
?
High AC in GnomAd at 29 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN2 | NM_002828.4 | c.279A>G | p.Thr93= | synonymous_variant | 4/9 | ENST00000309660.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN2 | ENST00000309660.10 | c.279A>G | p.Thr93= | synonymous_variant | 4/9 | 1 | NM_002828.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152140Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000128 AC: 32AN: 250934Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135596
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GnomAD4 exome AF: 0.000286 AC: 416AN: 1455428Hom.: 0 Cov.: 29 AF XY: 0.000294 AC XY: 213AN XY: 723966
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GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74314
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 11, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at