10-91939892-C-T

Position:

• chr10-91939892-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.139-60C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 1,131,650 control chromosomes in the GnomAD database, including 1,082 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.055 (665 hom., cov: 32)
  • Exomes 𝑓: 0.0082 (417 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0820

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=-0.75).
• BP6: Variant 10-91939892-C-T is Benign according to our data. Variant chr10-91939892-C-T is described in ClinVar as [Benign]. Clinvar id is 1178514.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3	c.139-60C>T		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12	c.139-60C>T		intron_variant		1	NM_003972.3	P1

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8357 AN: 152088 Hom.: 666 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0238

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00172

Gnomad OTH AF: 0.0473

GnomAD4 exome AF: 0.00818 AC: 8012 AN: 979444 Hom.: 417 AF XY: 0.00744 AC XY: 3729 AN XY: 501032

Gnomad4 AFR exome AF: 0.181

Gnomad4 AMR exome AF: 0.0137

Gnomad4 ASJ exome AF: 0.000925

Gnomad4 EAS exome AF: 0.0147

Gnomad4 SAS exome AF: 0.00809

Gnomad4 FIN exome AF: 0.0114

Gnomad4 NFE exome AF: 0.00115

Gnomad4 OTH exome AF: 0.0182

GnomAD4 genome AF: 0.0550 AC: 8372 AN: 152206 Hom.: 665 Cov.: 32 AF XY: 0.0535 AC XY: 3983 AN XY: 74422

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.00172

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0390 Hom.: 73

Bravo AF: 0.0604

Asia WGS AF: 0.0290 AC: 100 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

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.8
DANN	Benign	0.52

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: rs12241256; hg19: chr10-93699649;