chr10-92029510-T-C

Position:

• chr10-92029510-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003972.3(BTAF1):​c.*577T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.275 in 151,898 control chromosomes in the GnomAD database, including 7,011 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.27 (7009 hom., cov: 31)
  • Exomes 𝑓: 0.29 (2 hom.)
• Consequence: BTAF1 NM_003972.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.83

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.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.*577T>C		3_prime_UTR_variant	38/38	ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.*577T>C		3_prime_UTR_variant	38/38	1	NM_003972.3	ENSP00000265990	P1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41666 AN: 151640 Hom.: 7013 Cov.: 31

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.293 AC: 41 AN: 140 Hom.: 2 Cov.: 0 AF XY: 0.256 AC XY: 21 AN XY: 82

Gnomad4 FIN exome AF: 0.293

GnomAD4 genome AF: 0.275 AC: 41658 AN: 151758 Hom.: 7009 Cov.: 31 AF XY: 0.267 AC XY: 19826 AN XY: 74166

Gnomad4 AFR AF: 0.0900

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.317

Alfa AF: 0.343 Hom.: 3326

Bravo AF: 0.272

Asia WGS AF: 0.192 AC: 660 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.91

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: rs1914345; hg19: chr10-93789267;