chr10-91953648-T-G

Position:

• chr10-91953648-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate 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, single submitter B:1
• Conservation: PhyloP100: 0.0530

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 -14 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 id is 1290239.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3	c.565-89T>G		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12	c.565-89T>G		intron_variant		1	NM_003972.3	P1

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

Gnomad4 AFR exome AF: 0.0762

Gnomad4 AMR exome AF: 0.478

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.484

Gnomad4 SAS exome AF: 0.503

Gnomad4 FIN exome AF: 0.461

Gnomad4 NFE exome AF: 0.361

Gnomad4 OTH exome AF: 0.363

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

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.318

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: 0.322 Hom.: 1397

Bravo AF: 0.281

Asia WGS AF: 0.491 AC: 1705 AN: 3478

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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

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