10-91942216-T-A

Variant names:

• chr10-91942216-T-A
• rs12569736
• NM_003972.3:c.254-206T>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003972.3(BTAF1):​c.254-206T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,704 control chromosomes in the GnomAD database, including 8,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (8521 hom., cov: 31)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.59
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 10-91942216-T-A is Benign according to our data. Variant chr10-91942216-T-A is described in ClinVar as Benign. ClinVar VariationId is 1266434.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003972.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	NM_003972.3	MANE Select	c.254-206T>A		intron	N/A	NP_003963.1	Q2M1V9
	BTAF1	NR_165090.1		n.561-206T>A		intron	N/A
	BTAF1	NR_165091.1		n.561-206T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	ENST00000265990.12	TSL:1 MANE Select	c.254-206T>A		intron	N/A	ENSP00000265990.6	O14981-1
	BTAF1	ENST00000928671.1		c.254-206T>A		intron	N/A	ENSP00000598730.1
	BTAF1	ENST00000928669.1		c.253+2150T>A		intron	N/A	ENSP00000598728.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45817 AN: 151584 Hom.: 8508 Cov.: 31

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.302 AC: 45852 AN: 151704 Hom.: 8521 Cov.: 31 AF XY: 0.314 AC XY: 23296 AN XY: 74126

African (AFR) AF: 0.0892 AC: 3693 AN: 41386

American (AMR) AF: 0.385 AC: 5859 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1101 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2547 AN: 5140

South Asian (SAS) AF: 0.517 AC: 2486 AN: 4806

European-Finnish (FIN) AF: 0.466 AC: 4877 AN: 10468

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24274 AN: 67892

Other (OTH) AF: 0.284 AC: 599 AN: 2110

Alfa AF: 0.331 Hom.: 1134

Bravo AF: 0.282

Asia WGS AF: 0.492 AC: 1708 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.57
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12569736; hg19: chr10-93701973;