10-92029510-T-C

Variant names:

• chr10-92029510-T-C
• rs1914345
• NM_003972.3:c.*577T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003972.3(BTAF1):​c.*577T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.275 in 151,898 control chromosomes in the GnomAD database, including 7,011 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.27 (7009 hom., cov: 31)
  • Exomes 𝑓: 0.29 (2 hom.)
• Consequence: BTAF1 NM_003972.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.83
• Publications: 7 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTAF1	NM_003972.3	c.*577T>C		3_prime_UTR_variant	Exon 38 of 38	ENST00000265990.12	NP_003963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTAF1	ENST00000265990.12	c.*577T>C		3_prime_UTR_variant	Exon 38 of 38	1	NM_003972.3	ENSP00000265990.6

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41666 AN: 151640 Hom.: 7013 Cov.: 31

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.293 AC: 41 AN: 140 Hom.: 2 Cov.: 0 AF XY: 0.256 AC XY: 21 AN XY: 82

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.293 AC: 41 AN: 140

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.275 AC: 41658 AN: 151758 Hom.: 7009 Cov.: 31 AF XY: 0.267 AC XY: 19826 AN XY: 74166

African (AFR) AF: 0.0900 AC: 3734 AN: 41484

American (AMR) AF: 0.269 AC: 4103 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3472

East Asian (EAS) AF: 0.277 AC: 1433 AN: 5180

South Asian (SAS) AF: 0.160 AC: 770 AN: 4822

European-Finnish (FIN) AF: 0.296 AC: 3106 AN: 10494

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25846 AN: 67770

Other (OTH) AF: 0.317 AC: 668 AN: 2106

Alfa AF: 0.332 Hom.: 3506

Bravo AF: 0.272

Asia WGS AF: 0.192 AC: 660 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.91
PhyloP100		4.8
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: rs1914345; hg19: chr10-93789267;