Variant 10-91942298-T-TTGTGTGTG 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.254-98_254-91dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0532 in 543,078 control chromosomes in the GnomAD database, including 652 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.074 ( 571 hom., cov: 0)

Exomes 𝑓: 0.045 ( 81 hom. )

Consequence

BTAF1
NM_003972.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.01

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-T-TTGTGTGTG is Benign according to our data. Variant chr10-91942298-T-TTGTGTGTG is described in ClinVar as [Benign]. Clinvar id is 1288738.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.149 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.254-98_254-91dup		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12 linkuse as main transcript	c.254-98_254-91dup		intron_variant		1	NM_003972.3	P1	O14981-1

Frequencies

GnomAD3 genomes

AF:

0.0739

AC:

10885

AN:

147240

Hom.:

572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0180

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0482

Gnomad MID

AF:

0.0994

Gnomad NFE

AF:

0.0847

Gnomad OTH

AF:

0.0777

GnomAD4 exome

AF:

0.0455

AC:

17988

AN:

395732

Hom.:

AF XY:

0.0467

AC XY:

9639

AN XY:

206622

show subpopulations

Gnomad4 AFR exome

AF:

0.00736

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.0271

Gnomad4 EAS exome

AF:

0.0732

Gnomad4 SAS exome

AF:

0.0747

Gnomad4 FIN exome

AF:

0.0355

Gnomad4 NFE exome

AF:

0.0397

Gnomad4 OTH exome

AF:

0.0423

GnomAD4 genome

AF:

0.0739

AC:

10883

AN:

147346

Hom.:

571

Cov.:

AF XY:

0.0742

AC XY:

5297

AN XY:

71410

show subpopulations

Gnomad4 AFR

AF:

0.0180

Gnomad4 AMR

AF:

0.154

Gnomad4 ASJ

AF:

0.0579

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.107

Gnomad4 FIN

AF:

0.0482

Gnomad4 NFE

AF:

0.0847

Gnomad4 OTH

AF:

0.0764

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