8-140658761-A-T
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001352702.2(PTK2):c.*705T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 221,350 control chromosomes in the GnomAD database, including 20,514 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.39 ( 12839 hom., cov: 32)
Exomes 𝑓: 0.46 ( 7675 hom. )
Consequence
PTK2
NM_001352702.2 3_prime_UTR
NM_001352702.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.831
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 -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 8-140658761-A-T is Benign according to our data. Variant chr8-140658761-A-T is described in ClinVar as [Benign]. Clinvar id is 1226102.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTK2 | NM_001352702.2 | c.*705T>A | 3_prime_UTR_variant | 36/36 | ENST00000696786.1 | NP_001339631.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTK2 | ENST00000696786.1 | c.*705T>A | 3_prime_UTR_variant | 36/36 | NM_001352702.2 | ENSP00000512868.1 |
Frequencies
GnomAD3 genomes AF: 0.389 AC: 59043AN: 151950Hom.: 12828 Cov.: 32
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GnomAD4 exome AF: 0.460 AC: 31872AN: 69282Hom.: 7675 Cov.: 0 AF XY: 0.469 AC XY: 15027AN XY: 32052
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GnomAD4 genome AF: 0.388 AC: 59065AN: 152068Hom.: 12839 Cov.: 32 AF XY: 0.388 AC XY: 28812AN XY: 74314
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 18, 2020 | This variant is associated with the following publications: (PMID: 24930376) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at