chr10-91980672-T-C

Variant names:

• chr10-91980672-T-C
• rs2792022
• NM_003972.3:c.1755+114T>C

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.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
• Publications: 10 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=-0.87).
• BP6: Variant 10-91980672-T-C is Benign according to our data. Variant chr10-91980672-T-C is described in ClinVar as Benign. ClinVar VariationId 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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	NM_003972.3	MANE Select	c.1755+114T>C		intron	N/A	NP_003963.1
	BTAF1	NR_165090.1		n.2062+114T>C		intron	N/A
	BTAF1	NR_165091.1		n.2190+114T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	ENST00000265990.12	TSL:1 MANE Select	c.1755+114T>C		intron	N/A	ENSP00000265990.6
	BTAF1	ENST00000471217.5	TSL:1	n.1089+114T>C		intron	N/A
	BTAF1	ENST00000476401.1	TSL:3	n.39+114T>C		intron	N/A

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

African (AFR) AF: 0.0731 AC: 1182 AN: 16166

American (AMR) AF: 0.436 AC: 13389 AN: 30682

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 5322 AN: 18612

East Asian (EAS) AF: 0.487 AC: 15693 AN: 32198

South Asian (SAS) AF: 0.451 AC: 26467 AN: 58724

European-Finnish (FIN) AF: 0.393 AC: 14486 AN: 36882

Middle Eastern (MID) AF: 0.253 AC: 851 AN: 3368

European-Non Finnish (NFE) AF: 0.284 AC: 112448 AN: 396170

Other (OTH) AF: 0.301 AC: 9767 AN: 32402

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

African (AFR) AF: 0.0769 AC: 3194 AN: 41540

American (AMR) AF: 0.352 AC: 5378 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2502 AN: 5172

South Asian (SAS) AF: 0.476 AC: 2293 AN: 4822

European-Finnish (FIN) AF: 0.405 AC: 4283 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19045 AN: 67926

Other (OTH) AF: 0.243 AC: 514 AN: 2112

Alfa AF: 0.275 Hom.: 10511

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.56
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: rs2792022; hg19: chr10-93740429;