chr10-91935553-C-T

Variant names:

• chr10-91935553-C-T
• rs72823185
• NM_003972.3:c.15-104C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003972.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	NM_003972.3	MANE Select	c.15-104C>T		intron	N/A	NP_003963.1	Q2M1V9
	BTAF1	NR_165090.1		n.322-104C>T		intron	N/A
	BTAF1	NR_165091.1		n.322-104C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	ENST00000265990.12	TSL:1 MANE Select	c.15-104C>T		intron	N/A	ENSP00000265990.6	O14981-1
	BTAF1	ENST00000928671.1		c.15-104C>T		intron	N/A	ENSP00000598730.1
	BTAF1	ENST00000928669.1		c.15-104C>T		intron	N/A	ENSP00000598728.1

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

African (AFR) AF: 0.0320 AC: 803 AN: 25074

American (AMR) AF: 0.0880 AC: 2534 AN: 28810

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 3297 AN: 18232

East Asian (EAS) AF: 0.00511 AC: 184 AN: 35980

South Asian (SAS) AF: 0.141 AC: 7077 AN: 50096

European-Finnish (FIN) AF: 0.143 AC: 6092 AN: 42460

Middle Eastern (MID) AF: 0.190 AC: 757 AN: 3990

European-Non Finnish (NFE) AF: 0.166 AC: 138032 AN: 833608

Other (OTH) AF: 0.148 AC: 6711 AN: 45362

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

African (AFR) AF: 0.0354 AC: 1471 AN: 41528

American (AMR) AF: 0.126 AC: 1925 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5182

South Asian (SAS) AF: 0.138 AC: 664 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1529 AN: 10586

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11454 AN: 67986

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.0586 Hom.: 86

Bravo AF: 0.113

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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