chr10-91942648-C-T

Position:

• chr10-91942648-C-T

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.400+80C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,440,926 control chromosomes in the GnomAD database, including 103,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (8889 hom., cov: 31)
  • Exomes 𝑓: 0.38 (94433 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.318

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=-0.91).
• BP6: Variant 10-91942648-C-T is Benign according to our data. Variant chr10-91942648-C-T is described in ClinVar as [Benign]. Clinvar id is 1234034.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3	c.400+80C>T		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12	c.400+80C>T		intron_variant		1	NM_003972.3	P1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48506 AN: 151898 Hom.: 8874 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.379 AC: 487960 AN: 1288910 Hom.: 94433 AF XY: 0.381 AC XY: 244213 AN XY: 640660

Gnomad4 AFR exome AF: 0.134

Gnomad4 AMR exome AF: 0.472

Gnomad4 ASJ exome AF: 0.337

Gnomad4 EAS exome AF: 0.491

Gnomad4 SAS exome AF: 0.505

Gnomad4 FIN exome AF: 0.462

Gnomad4 NFE exome AF: 0.366

Gnomad4 OTH exome AF: 0.370

GnomAD4 genome AF: 0.319 AC: 48544 AN: 152016 Hom.: 8889 Cov.: 31 AF XY: 0.331 AC XY: 24587 AN XY: 74260

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.301

Alfa AF: 0.323 Hom.: 1862

Bravo AF: 0.301

Asia WGS AF: 0.499 AC: 1732 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	-0.91
CADD	Benign	4.0
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3814640; hg19: chr10-93702405; COSMIC: COSV56431265;