rs1056726
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001382273.1(TNK2):c.1764C>T(p.Phe588=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 1,564,262 control chromosomes in the GnomAD database, including 3,206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.061 ( 332 hom., cov: 33)
Exomes 𝑓: 0.061 ( 2874 hom. )
Consequence
TNK2
NM_001382273.1 synonymous
NM_001382273.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.821
Genes affected
TNK2 (HGNC:19297): (tyrosine kinase non receptor 2) This gene encodes a tyrosine kinase that binds Cdc42Hs in its GTP-bound form and inhibits both the intrinsic and GTPase-activating protein (GAP)-stimulated GTPase activity of Cdc42Hs. This binding is mediated by a unique sequence of 47 amino acids C-terminal to an SH3 domain. The protein may be involved in a regulatory mechanism that sustains the GTP-bound active form of Cdc42Hs and which is directly linked to a tyrosine phosphorylation signal transduction pathway. Several alternatively spliced transcript variants have been identified from this gene, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 3-195868534-G-A is Benign according to our data. Variant chr3-195868534-G-A is described in ClinVar as [Benign]. Clinvar id is 259872.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.821 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNK2 | NM_001382273.1 | c.1764C>T | p.Phe588= | synonymous_variant | 13/16 | ENST00000672887.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNK2 | ENST00000672887.2 | c.1764C>T | p.Phe588= | synonymous_variant | 13/16 | NM_001382273.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0607 AC: 9231AN: 152090Hom.: 332 Cov.: 33
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GnomAD3 exomes AF: 0.0544 AC: 9235AN: 169668Hom.: 290 AF XY: 0.0553 AC XY: 5273AN XY: 95316
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GnomAD4 exome AF: 0.0610 AC: 86078AN: 1412054Hom.: 2874 Cov.: 45 AF XY: 0.0609 AC XY: 42674AN XY: 701090
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GnomAD4 genome ? AF: 0.0607 AC: 9242AN: 152208Hom.: 332 Cov.: 33 AF XY: 0.0602 AC XY: 4479AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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