Variant 10-91942298-TTGTGTG-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.254-96_254-91del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 543,692 control chromosomes in the GnomAD database, including 20,271 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 12127 hom., cov: 0)

Exomes 𝑓: 0.37 ( 8144 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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-91942298-TTGTGTG-T is Benign according to our data. Variant chr10-91942298-TTGTGTG-T is described in ClinVar as [Benign]. Clinvar id is 1265763.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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.254-96_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.254-96_254-91del		intron_variant		1	NM_003972.3	P1	O14981-1

Frequencies

GnomAD3 genomes

AF:

0.408

AC:

60020

AN:

147138

Hom.:

12129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.394

Gnomad NFE

AF:

0.443

Gnomad OTH

AF:

0.439

GnomAD4 exome

AF:

0.366

AC:

144924

AN:

396448

Hom.:

8144

AF XY:

0.363

AC XY:

75146

AN XY:

207022

show subpopulations

Gnomad4 AFR exome

AF:

0.277

Gnomad4 AMR exome

AF:

0.337

Gnomad4 ASJ exome

AF:

0.358

Gnomad4 EAS exome

AF:

0.413

Gnomad4 SAS exome

AF:

0.295

Gnomad4 FIN exome

AF:

0.354

Gnomad4 NFE exome

AF:

0.378

Gnomad4 OTH exome

AF:

0.360

GnomAD4 genome

AF:

0.408

AC:

60035

AN:

147244

Hom.:

12127

Cov.:

AF XY:

0.403

AC XY:

28785

AN XY:

71344

show subpopulations

Gnomad4 AFR

AF:

0.344

Gnomad4 AMR

AF:

0.409

Gnomad4 ASJ

AF:

0.449

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.334

Gnomad4 FIN

AF:

0.395

Gnomad4 NFE

AF:

0.443

Gnomad4 OTH

AF:

0.442

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