10-91942298-TTGTGTGTGTGTG-T

Position:

• chr10-91942298-TTGTGTGTGTGTG-T

Variant summary

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

The NM_003972.3(BTAF1):​c.254-102_254-91del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 546,326 control chromosomes in the GnomAD database, including 5,176 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1550 hom., cov: 0)
  • Exomes 𝑓: 0.18 (3626 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.36

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-TTGTGTGTGTGTG-T is Benign according to our data. Variant chr10-91942298-TTGTGTGTGTGTG-T is described in ClinVar as [Benign]. Clinvar id is 1240855.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.254-102_254-91del		intron_variant		ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.254-102_254-91del		intron_variant		1	NM_003972.3	ENSP00000265990	P1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 20835 AN: 147308 Hom.: 1548 Cov.: 0

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.183 AC: 73107 AN: 398912 Hom.: 3626 AF XY: 0.182 AC XY: 37952 AN XY: 208328

Gnomad4 AFR exome AF: 0.117

Gnomad4 AMR exome AF: 0.116

Gnomad4 ASJ exome AF: 0.210

Gnomad4 EAS exome AF: 0.00539

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.207

Gnomad4 OTH exome AF: 0.182

GnomAD4 genome AF: 0.141 AC: 20844 AN: 147414 Hom.: 1550 Cov.: 0 AF XY: 0.141 AC XY: 10042 AN XY: 71444

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.158

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;