17-47698708-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001394755.1(TBKBP1):c.567C>T(p.Pro189Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000791 in 1,607,584 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00058 ( 4 hom. )
Consequence
TBKBP1
NM_001394755.1 synonymous
NM_001394755.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.594
Genes affected
TBKBP1 (HGNC:30140): (TBK1 binding protein 1) TBKBP1 is an adaptor protein that binds to TBK1 (MIM 604834) and is part of the interaction network in the TNF (MIM 191160)/NFKB (see MIM 164011) pathway (Bouwmeester et al., 2004 [PubMed 14743216]).[supplied by OMIM, Mar 2008]
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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=-0.68).
BP6
Variant 17-47698708-C-T is Benign according to our data. Variant chr17-47698708-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647876.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.594 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBKBP1 | NM_001394755.1 | c.567C>T | p.Pro189Pro | synonymous_variant | Exon 5 of 10 | ENST00000578982.6 | NP_001381684.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBKBP1 | ENST00000578982.6 | c.567C>T | p.Pro189Pro | synonymous_variant | Exon 5 of 10 | 3 | NM_001394755.1 | ENSP00000462339.2 | ||
TBKBP1 | ENST00000361722.7 | c.567C>T | p.Pro189Pro | synonymous_variant | Exon 4 of 9 | 1 | ENSP00000354777.3 | |||
TBKBP1 | ENST00000537587.6 | c.567C>T | p.Pro189Pro | synonymous_variant | Exon 5 of 5 | 3 | ENSP00000446365.2 |
Frequencies
GnomAD3 genomes AF: 0.00285 AC: 433AN: 152142Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000972 AC: 231AN: 237570Hom.: 1 AF XY: 0.000784 AC XY: 101AN XY: 128764
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GnomAD4 exome AF: 0.000575 AC: 837AN: 1455324Hom.: 4 Cov.: 32 AF XY: 0.000535 AC XY: 387AN XY: 723348
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GnomAD4 genome AF: 0.00286 AC: 435AN: 152260Hom.: 0 Cov.: 31 AF XY: 0.00282 AC XY: 210AN XY: 74452
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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
Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
TBKBP1: BP4, BP7 -
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