Variant 10-91942298-TTGTGTGTGTGTG-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003972.3(BTAF1):c.254-102_254-91del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 546,326 control chromosomes in the GnomAD database, including 5,176 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1550 hom., cov: 0)

Exomes 𝑓: 0.18 ( 3626 hom. )

Consequence

BTAF1
NM_003972.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.36

Variant links:

Genes affected

BTAF1 (HGNC:17307): (B-TFIID TATA-box binding protein associated factor 1) This gene encodes a TAF (TATA box-binding protein-associated factor), which associates with TBP (TATA box-binding protein) to form the B-TFIID complex that is required for transcription initiation of genes by RNA polymerase II. This TAF has DNA-dependent ATPase activity, which drives the dissociation of TBP from DNA, freeing the TBP to associate with other TATA boxes or TATA-less promoters. [provided by RefSeq, Sep 2011]

BTAF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-91942298-TTGTGTGTGTGTG-T is Benign according to our data. Variant chr10-91942298-TTGTGTGTGTGTG-T is described in ClinVar as [Benign]. Clinvar id is 1240855.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3 linkuse as main transcript	c.254-102_254-91del		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12 linkuse as main transcript	c.254-102_254-91del		intron_variant		1	NM_003972.3	P1	O14981-1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

20835

AN:

147308

Hom.:

1548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.0120

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.159

GnomAD4 exome

AF:

0.183

AC:

73107

AN:

398912

Hom.:

3626

AF XY:

0.182

AC XY:

37952

AN XY:

208328

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.116

Gnomad4 ASJ exome

AF:

0.210

Gnomad4 EAS exome

AF:

0.00539

Gnomad4 SAS exome

AF:

0.158

Gnomad4 FIN exome

AF:

0.174

Gnomad4 NFE exome

AF:

0.207

Gnomad4 OTH exome

AF:

0.182

GnomAD4 genome

AF:

0.141

AC:

20844

AN:

147414

Hom.:

1550

Cov.:

AF XY:

0.141

AC XY:

10042

AN XY:

71444

show subpopulations

Gnomad4 AFR

AF:

0.103

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.0120

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.169

Gnomad4 OTH

AF:

0.158

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

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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