Variant 10-91942298-T-TTG 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.254-92_254-91dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 544,822 control chromosomes in the GnomAD database, including 120 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.034 ( 117 hom., cov: 0)

Exomes 𝑓: 0.017 ( 3 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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-91942298-T-TTG is Benign according to our data. Variant chr10-91942298-T-TTG is described in ClinVar as [Benign]. Clinvar id is 1245501.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.071 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.254-92_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.254-92_254-91dup		intron_variant		1	NM_003972.3	P1	O14981-1

Frequencies

GnomAD3 genomes

AF:

0.0340

AC:

5002

AN:

147270

Hom.:

118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0732

Gnomad AMI

AF:

0.0342

Gnomad AMR

AF:

0.0195

Gnomad ASJ

AF:

0.0404

Gnomad EAS

AF:

0.00600

Gnomad SAS

AF:

0.0267

Gnomad FIN

AF:

0.00665

Gnomad MID

AF:

0.0224

Gnomad NFE

AF:

0.0199

Gnomad OTH

AF:

0.0371

GnomAD4 exome

AF:

0.0170

AC:

6763

AN:

397446

Hom.:

AF XY:

0.0173

AC XY:

3601

AN XY:

207564

show subpopulations

Gnomad4 AFR exome

AF:

0.0487

Gnomad4 AMR exome

AF:

0.0170

Gnomad4 ASJ exome

AF:

0.0258

Gnomad4 EAS exome

AF:

0.0160

Gnomad4 SAS exome

AF:

0.0263

Gnomad4 FIN exome

AF:

0.0169

Gnomad4 NFE exome

AF:

0.0140

Gnomad4 OTH exome

AF:

0.0202

GnomAD4 genome

AF:

0.0340

AC:

5009

AN:

147376

Hom.:

117

Cov.:

AF XY:

0.0333

AC XY:

2380

AN XY:

71438

show subpopulations

Gnomad4 AFR

AF:

0.0732

Gnomad4 AMR

AF:

0.0195

Gnomad4 ASJ

AF:

0.0404

Gnomad4 EAS

AF:

0.00601

Gnomad4 SAS

AF:

0.0265

Gnomad4 FIN

AF:

0.00665

Gnomad4 NFE

AF:

0.0199

Gnomad4 OTH

AF:

0.0367

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 20, 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