chr10-91935553-C-T

Position:

• chr10-91935553-C-T

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.15-104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,235,778 control chromosomes in the GnomAD database, including 15,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1401 hom., cov: 32)
  • Exomes 𝑓: 0.15 (13785 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=-0.91).
• BP6: Variant 10-91935553-C-T is Benign according to our data. Variant chr10-91935553-C-T is described in ClinVar as [Benign]. Clinvar id is 1278473.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.15-104C>T		intron_variant		ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.15-104C>T		intron_variant		1	NM_003972.3	ENSP00000265990.6

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18212 AN: 152048 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.142

GnomAD4 exome AF: 0.153 AC: 165487 AN: 1083612 Hom.: 13785 AF XY: 0.154 AC XY: 82686 AN XY: 537800

Gnomad4 AFR exome AF: 0.0320

Gnomad4 AMR exome AF: 0.0880

Gnomad4 ASJ exome AF: 0.181

Gnomad4 EAS exome AF: 0.00511

Gnomad4 SAS exome AF: 0.141

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.148

GnomAD4 genome AF: 0.120 AC: 18202 AN: 152166 Hom.: 1401 Cov.: 32 AF XY: 0.119 AC XY: 8828 AN XY: 74398

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0586 Hom.: 86

Bravo AF: 0.113

Asia WGS AF: 0.0780 AC: 272 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	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.71

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: rs72823185; hg19: chr10-93695310; COSMIC: COSV56440989;