Variant 17-47696785-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001394755.1(TBKBP1):c.300G>A(p.Glu100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,613,982 control chromosomes in the GnomAD database, including 229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0038 ( 23 hom., cov: 31)

Exomes 𝑓: 0.0031 ( 206 hom. )

Consequence

TBKBP1
NM_001394755.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.42

Variant links:

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]

TBKBP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 17-47696785-G-A is Benign according to our data. Variant chr17-47696785-G-A is described in ClinVar as [Benign]. Clinvar id is 779977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.42 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBKBP1	NM_001394755.1 linkuse as main transcript	c.300G>A	p.Glu100=	synonymous_variant	3/10	ENST00000578982.6	NP_001381684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBKBP1	ENST00000578982.6 linkuse as main transcript	c.300G>A	p.Glu100=	synonymous_variant	3/10	3	NM_001394755.1	ENSP00000462339	P1	A7MCY6-1
TBKBP1	ENST00000361722.7 linkuse as main transcript	c.300G>A	p.Glu100=	synonymous_variant	2/9	1		ENSP00000354777	P1	A7MCY6-1
TBKBP1	ENST00000537587.6 linkuse as main transcript	c.300G>A	p.Glu100=	synonymous_variant	3/5	3		ENSP00000446365

Frequencies

GnomAD3 genomes

AF:

0.00380

AC:

579

AN:

152234

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000723

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0985

Gnomad SAS

AF:

0.00744

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00856

AC:

2131

AN:

248888

Hom.:

109

AF XY:

0.00797

AC XY:

1076

AN XY:

135062

show subpopulations

Gnomad AFR exome

AF:

0.000130

Gnomad AMR exome

AF:

0.000174

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.108

Gnomad SAS exome

AF:

0.00458

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.000177

Gnomad OTH exome

AF:

0.00430

GnomAD4 exome

AF:

0.00314

AC:

4587

AN:

1461630

Hom.:

206

Cov.:

AF XY:

0.00314

AC XY:

2282

AN XY:

727116

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.000134

Gnomad4 ASJ exome

AF:

0.000344

Gnomad4 EAS exome

AF:

0.0955

Gnomad4 SAS exome

AF:

0.00468

Gnomad4 FIN exome

AF:

0.0000562

Gnomad4 NFE exome

AF:

0.0000926

Gnomad4 OTH exome

AF:

0.00437

GnomAD4 genome

AF:

0.00381

AC:

581

AN:

152352

Hom.:

Cov.:

AF XY:

0.00426

AC XY:

317

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.0000721

Gnomad4 AMR

AF:

0.000653

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0989

Gnomad4 SAS

AF:

0.00745

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000206

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.000481

Hom.:

Bravo

AF:

0.00425

Asia WGS

AF:

0.0290

AC:

102

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.000296

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 14, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

9.9

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over