10-91942298-T-TTGTGTGTG

Position:

• chr10-91942298-T-TTGTGTGTG

Variant summary

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

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.01

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 10-91942298-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	Protein	UniProt
BTAF1	NM_003972.3	c.254-98_254-91dup		intron_variant		ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.254-98_254-91dup		intron_variant		1	NM_003972.3	ENSP00000265990	P1

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 10885 AN: 147240 Hom.: 572 Cov.: 0

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.: 81 AF XY: 0.0467 AC XY: 9639 AN XY: 206622

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.: 0 AF XY: 0.0742 AC XY: 5297 AN XY: 71410

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs58443276; hg19: chr10-93702055;