rs833372

Positions:

• chr10-92015616-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003972.3(BTAF1):​c.4585-724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 150,526 control chromosomes in the GnomAD database, including 8,523 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 0.31 (8523 hom., cov: 32)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3	c.4585-724A>G		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12	c.4585-724A>G		intron_variant		1	NM_003972.3	P1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 45901 AN: 150406 Hom.: 8511 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.286

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.305 AC: 45933 AN: 150526 Hom.: 8523 Cov.: 32 AF XY: 0.317 AC XY: 23361 AN XY: 73608

Gnomad4 AFR AF: 0.0930

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.285

Alfa AF: 0.332 Hom.: 1120

Bravo AF: 0.281

Asia WGS AF: 0.490 AC: 1701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.62

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: rs833372; hg19: chr10-93775373;