10-91942298-T-TTGTGTG

Position:

• chr10-91942298-T-TTGTGTG

Variant summary

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

The NM_003972.3(BTAF1):​c.254-96_254-91dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0947 in 392,820 control chromosomes in the GnomAD database, including 202 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1399 hom., cov: 0)
  • Exomes 𝑓: 0.095 (202 hom.)
  • Failed GnomAD Quality Control
• 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-TTGTGTG is Benign according to our data. Variant chr10-91942298-T-TTGTGTG is described in ClinVar as [Benign]. Clinvar id is 1247181.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.254-96_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.254-96_254-91dup		intron_variant		1	NM_003972.3	ENSP00000265990	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 18279 AN: 147118 Hom.: 1396 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.116

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.0947 AC: 37217 AN: 392820 Hom.: 202 AF XY: 0.0989 AC XY: 20273 AN XY: 205086

Gnomad4 AFR exome AF: 0.0191

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.0944

Gnomad4 EAS exome AF: 0.159

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.120

Gnomad4 NFE exome AF: 0.0800

Gnomad4 OTH exome AF: 0.0929

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.124 AC: 18290 AN: 147222 Hom.: 1399 Cov.: 0 AF XY: 0.130 AC XY: 9257 AN XY: 71328

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.117

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;