chr10-91942686-G-A

Position:

• chr10-91942686-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003972.3(BTAF1):​c.400+118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,196,296 control chromosomes in the GnomAD database, including 84,034 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.30 (8530 hom., cov: 32)
  • Exomes 𝑓: 0.37 (75504 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.670

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 10-91942686-G-A is Benign according to our data. Variant chr10-91942686-G-A is described in ClinVar as [Benign]. Clinvar id is 1243130.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3	c.400+118G>A		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12	c.400+118G>A		intron_variant		1	NM_003972.3	P1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45926 AN: 151986 Hom.: 8517 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.373 AC: 389954 AN: 1044192 Hom.: 75504 AF XY: 0.377 AC XY: 195202 AN XY: 518182

Gnomad4 AFR exome AF: 0.0775

Gnomad4 AMR exome AF: 0.453

Gnomad4 ASJ exome AF: 0.329

Gnomad4 EAS exome AF: 0.492

Gnomad4 SAS exome AF: 0.502

Gnomad4 FIN exome AF: 0.459

Gnomad4 NFE exome AF: 0.364

Gnomad4 OTH exome AF: 0.362

GnomAD4 genome AF: 0.302 AC: 45960 AN: 152104 Hom.: 8530 Cov.: 32 AF XY: 0.314 AC XY: 23363 AN XY: 74340

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.284

Alfa AF: 0.331 Hom.: 1133

Bravo AF: 0.281

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.88
CADD	Benign	1.5
DANN	Benign	0.50

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: rs3814639; hg19: chr10-93702443; COSMIC: COSV56431273;