Variant 14-93246298-TAAAA-TAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001002860.4(BTBD7):c.2122-13delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 108 hom., cov: 0)

Exomes 𝑓: 0.24 ( 18 hom. )

Failed GnomAD Quality Control

Consequence

BTBD7
NM_001002860.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.796

Variant links:

Genes affected

BTBD7 (HGNC:18269): (BTB domain containing 7) Predicted to be involved in regulation of branching involved in salivary gland morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

BTBD7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 14-93246298-TA-T is Benign according to our data. Variant chr14-93246298-TA-T is described in ClinVar as [Benign]. Clinvar id is 402435.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD7	NM_001002860.4 link	c.2122-13delT		intron_variant	Intron 9 of 10	ENST00000334746.10	NP_001002860.2	Q9P203-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BTBD7	ENST00000334746.10 link	c.2122-13delT	intron_variant	Intron 9 of 10	1	NM_001002860.4	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5 link	c.1069-13delT	intron_variant	Intron 7 of 8	1		ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000553975.1 link	c.967-13delT	intron_variant	Intron 5 of 6	2		ENSP00000450778.1	H0YJ41
BTBD7	ENST00000355125.3 link	n.*743-13delT	intron_variant	Intron 6 of 7	2		ENSP00000347246.3	H3BLV3

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

24022

AN:

138108

Hom.:

107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.122

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.163

GnomAD3 exomes

AF:

0.272

AC:

29394

AN:

108090

Hom.:

AF XY:

0.274

AC XY:

16045

AN XY:

58568

show subpopulations

Gnomad AFR exome

AF:

0.211

Gnomad AMR exome

AF:

0.318

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.290

Gnomad SAS exome

AF:

0.241

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.239

AC:

263344

AN:

1103622

Hom.:

Cov.:

AF XY:

0.237

AC XY:

127078

AN XY:

535736

show subpopulations

Gnomad4 AFR exome

AF:

0.190

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.226

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.230

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.174

AC:

24045

AN:

138192

Hom.:

108

Cov.:

AF XY:

0.179

AC XY:

12037

AN XY:

67138

show subpopulations

Gnomad4 AFR

AF:

0.166

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.199

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.165

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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