8-140706179-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001352702.2(PTK2):c.2292G>A(p.Pro764=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,314 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 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000075 ( 0 hom. )
Consequence
PTK2
NM_001352702.2 synonymous
NM_001352702.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.13
Genes affected
PTK2 (HGNC:9611): (protein tyrosine kinase 2) This gene encodes a cytoplasmic protein tyrosine kinase which is found concentrated in the focal adhesions that form between cells growing in the presence of extracellular matrix constituents. The encoded protein is a member of the FAK subfamily of protein tyrosine kinases but lacks significant sequence similarity to kinases from other subfamilies. Activation of this gene may be an important early step in cell growth and intracellular signal transduction pathways triggered in response to certain neural peptides or to cell interactions with the extracellular matrix. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017]
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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=-0.71).
BP6
?
Variant 8-140706179-C-T is Benign according to our data. Variant chr8-140706179-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658869.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.13 with no splicing effect.
BS2
?
High AC in GnomAd at 18 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTK2 | NM_001352702.2 | c.2292G>A | p.Pro764= | synonymous_variant | 27/36 | ENST00000696786.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTK2 | ENST00000696786.1 | c.2292G>A | p.Pro764= | synonymous_variant | 27/36 | NM_001352702.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152128Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000159 AC: 40AN: 251420Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135888
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GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461186Hom.: 0 Cov.: 30 AF XY: 0.0000798 AC XY: 58AN XY: 726952
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | PTK2: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at