10-91980672-T-C

Position:

• chr10-91980672-T-C

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.1755+114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 777,280 control chromosomes in the GnomAD database, including 40,253 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (6103 hom., cov: 32)
  • Exomes 𝑓: 0.32 (34150 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.10

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]

BTAF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 10-91980672-T-C is Benign according to our data. Variant chr10-91980672-T-C is described in ClinVar as [Benign]. Clinvar id is 1283430.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.1755+114T>C		intron_variant		ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.1755+114T>C		intron_variant		1	NM_003972.3	ENSP00000265990.6
BTAF1	ENST00000471217.5	n.1089+114T>C		intron_variant		1
BTAF1	ENST00000476401.1	n.39+114T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38414 AN: 151958 Hom.: 6088 Cov.: 32

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.319 AC: 199605 AN: 625204 Hom.: 34150 AF XY: 0.324 AC XY: 107473 AN XY: 331342

Gnomad4 AFR exome AF: 0.0731

Gnomad4 AMR exome AF: 0.436

Gnomad4 ASJ exome AF: 0.286

Gnomad4 EAS exome AF: 0.487

Gnomad4 SAS exome AF: 0.451

Gnomad4 FIN exome AF: 0.393

Gnomad4 NFE exome AF: 0.284

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.253 AC: 38453 AN: 152076 Hom.: 6103 Cov.: 32 AF XY: 0.266 AC XY: 19772 AN XY: 74324

Gnomad4 AFR AF: 0.0769

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.243

Alfa AF: 0.279 Hom.: 8717

Bravo AF: 0.236

Asia WGS AF: 0.475 AC: 1646 AN: 3476

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	-0.87
CADD	Benign	1.4
DANN	Benign	0.56

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: rs2792022; hg19: chr10-93740429;