Variant 17-47698785-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2

The NM_001394755.1(TBKBP1):c.634+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,538,430 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0078 ( 17 hom., cov: 31)

Exomes 𝑓: 0.00088 ( 14 hom. )

Consequence

TBKBP1
NM_001394755.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.759

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 17-47698785-C-T is Benign according to our data. Variant chr17-47698785-C-T is described in ClinVar as [Benign]. Clinvar id is 717513.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00776 (1180/152132) while in subpopulation AFR AF= 0.0273 (1131/41476). AF 95% confidence interval is 0.0259. There are 17 homozygotes in gnomad4. There are 546 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBKBP1	NM_001394755.1 linkuse as main transcript	c.634+10C>T		intron_variant		ENST00000578982.6	NP_001381684.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
TBKBP1	ENST00000578982.6 linkuse as main transcript	c.634+10C>T	intron_variant	3	NM_001394755.1	ENSP00000462339	P1	A7MCY6-1
TBKBP1	ENST00000361722.7 linkuse as main transcript	c.634+10C>T	intron_variant	1		ENSP00000354777	P1	A7MCY6-1
TBKBP1	ENST00000537587.6 linkuse as main transcript		downstream_gene_variant	3		ENSP00000446365

Frequencies

GnomAD3 genomes

AF:

0.00774

AC:

1176

AN:

152014

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0272

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00236

AC:

446

AN:

189266

Hom.:

AF XY:

0.00167

AC XY:

169

AN XY:

100970

show subpopulations

Gnomad AFR exome

AF:

0.0275

Gnomad AMR exome

AF:

0.00179

Gnomad ASJ exome

AF:

0.000192

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000162

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000181

Gnomad OTH exome

AF:

0.00156

GnomAD4 exome

AF:

0.000881

AC:

1221

AN:

1386298

Hom.:

Cov.:

AF XY:

0.000760

AC XY:

517

AN XY:

680194

show subpopulations

Gnomad4 AFR exome

AF:

0.0290

Gnomad4 AMR exome

AF:

0.00179

Gnomad4 ASJ exome

AF:

0.000137

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000146

Gnomad4 FIN exome

AF:

0.0000587

Gnomad4 NFE exome

AF:

0.0000944

Gnomad4 OTH exome

AF:

0.00210

GnomAD4 genome

AF:

0.00776

AC:

1180

AN:

152132

Hom.:

Cov.:

AF XY:

0.00734

AC XY:

546

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0273

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000191

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00647

Hom.:

Bravo

AF:

0.00908

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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