chr3-195888505-A-G
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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):āc.84T>Cā(p.Asp28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,612,956 control chromosomes in the GnomAD database, including 79,118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.39 ( 12905 hom., cov: 30)
Exomes š: 0.29 ( 66213 hom. )
Consequence
TNK2
NM_001382273.1 synonymous
NM_001382273.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.789
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 3-195888505-A-G is Benign according to our data. Variant chr3-195888505-A-G is described in ClinVar as [Benign]. Clinvar id is 259882.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.789 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNK2 | NM_001382273.1 | c.84T>C | p.Asp28= | synonymous_variant | 2/16 | ENST00000672887.2 | NP_001369202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNK2 | ENST00000672887.2 | c.84T>C | p.Asp28= | synonymous_variant | 2/16 | NM_001382273.1 | ENSP00000499899 |
Frequencies
GnomAD3 genomes AF: 0.388 AC: 58818AN: 151702Hom.: 12883 Cov.: 30
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GnomAD3 exomes AF: 0.337 AC: 84585AN: 250728Hom.: 15392 AF XY: 0.329 AC XY: 44618AN XY: 135524
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GnomAD4 exome AF: 0.294 AC: 428921AN: 1461136Hom.: 66213 Cov.: 36 AF XY: 0.292 AC XY: 212434AN XY: 726840
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GnomAD4 genome AF: 0.388 AC: 58893AN: 151820Hom.: 12905 Cov.: 30 AF XY: 0.387 AC XY: 28724AN XY: 74174
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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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