10-91942285-T-TA

Position:

• chr10-91942285-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003972.3(BTAF1):​c.254-127dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 589,186 control chromosomes in the GnomAD database, including 17,079 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.33 (8066 hom., cov: 20)
  • Exomes 𝑓: 0.26 (9013 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.729

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-91942285-T-TA is Benign according to our data. Variant chr10-91942285-T-TA is described in ClinVar as [Benign]. Clinvar id is 1263341.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.254-127dup		intron_variant		ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.254-127dup		intron_variant		1	NM_003972.3	ENSP00000265990	P1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 44134 AN: 134792 Hom.: 8054 Cov.: 20

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.255 AC: 115915 AN: 454278 Hom.: 9013 AF XY: 0.263 AC XY: 61988 AN XY: 235324

Gnomad4 AFR exome AF: 0.0687

Gnomad4 AMR exome AF: 0.342

Gnomad4 ASJ exome AF: 0.246

Gnomad4 EAS exome AF: 0.377

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.325

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.327 AC: 44166 AN: 134908 Hom.: 8066 Cov.: 20 AF XY: 0.341 AC XY: 22183 AN XY: 65114

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.335

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs67087052; hg19: chr10-93702042;