rs12571564

Variant names:

• chr10-91953648-T-G
• rs12571564
• NM_003972.3:c.565-89T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-91953648-T-G
• chr10-91953648-T-A
• chr10-91953648-T-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003972.3(BTAF1):​c.565-89T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 1,415,708 control chromosomes in the GnomAD database, including 99,422 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.30 (8529 hom., cov: 32)
  • Exomes 𝑓: 0.37 (90893 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0530
• Publications: 2 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 10-91953648-T-G is Benign according to our data. Variant chr10-91953648-T-G is described in ClinVar as Benign. ClinVar VariationId is 1290239.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 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.565-89T>G		intron	N/A	NP_003963.1	Q2M1V9
	BTAF1	NR_165090.1		n.872-89T>G		intron	N/A
	BTAF1	NR_165091.1		n.872-89T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	ENST00000265990.12	TSL:1 MANE Select	c.565-89T>G		intron	N/A	ENSP00000265990.6	O14981-1
	BTAF1	ENST00000928671.1		c.565-89T>G		intron	N/A	ENSP00000598730.1
	BTAF1	ENST00000928669.1		c.418-89T>G		intron	N/A	ENSP00000598728.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45933 AN: 151992 Hom.: 8518 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.372 AC: 470136 AN: 1263598 Hom.: 90893 AF XY: 0.375 AC XY: 236246 AN XY: 629186

African (AFR) AF: 0.0762 AC: 2139 AN: 28056

American (AMR) AF: 0.478 AC: 15119 AN: 31646

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 6834 AN: 20528

East Asian (EAS) AF: 0.484 AC: 18575 AN: 38398

South Asian (SAS) AF: 0.503 AC: 34619 AN: 68762

European-Finnish (FIN) AF: 0.461 AC: 22908 AN: 49654

Middle Eastern (MID) AF: 0.290 AC: 1479 AN: 5102

European-Non Finnish (NFE) AF: 0.361 AC: 349239 AN: 968478

Other (OTH) AF: 0.363 AC: 19224 AN: 52974

GnomAD4 genome AF: 0.302 AC: 45964 AN: 152110 Hom.: 8529 Cov.: 32 AF XY: 0.314 AC XY: 23370 AN XY: 74342

African (AFR) AF: 0.0897 AC: 3725 AN: 41538

American (AMR) AF: 0.385 AC: 5889 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2507 AN: 5152

South Asian (SAS) AF: 0.518 AC: 2499 AN: 4820

European-Finnish (FIN) AF: 0.467 AC: 4932 AN: 10566

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

European-Non Finnish (NFE) AF: 0.357 AC: 24289 AN: 67960

Other (OTH) AF: 0.285 AC: 602 AN: 2110

Alfa AF: 0.322 Hom.: 1397

Bravo AF: 0.281

Asia WGS AF: 0.491 AC: 1705 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		0.053
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: rs12571564; hg19: chr10-93713405; COSMIC: COSV56431283; COSMIC: COSV56431283;