chr10-91939892-C-T

Variant names:

• chr10-91939892-C-T
• rs12241256
• NM_003972.3:c.139-60C>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.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, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0820
• Publications: 2 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=-0.75).
• BP6: Variant 10-91939892-C-T is Benign according to our data. Variant chr10-91939892-C-T is described in ClinVar as Benign. ClinVar VariationId is 1178514.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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.139-60C>T		intron	N/A	NP_003963.1	Q2M1V9
	BTAF1	NR_165090.1		n.446-60C>T		intron	N/A
	BTAF1	NR_165091.1		n.446-60C>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.139-60C>T		intron	N/A	ENSP00000265990.6	O14981-1
	BTAF1	ENST00000928671.1		c.139-60C>T		intron	N/A	ENSP00000598730.1
	BTAF1	ENST00000928669.1		c.139-60C>T		intron	N/A	ENSP00000598728.1

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

African (AFR) AF: 0.181 AC: 4183 AN: 23122

American (AMR) AF: 0.0137 AC: 520 AN: 37848

Ashkenazi Jewish (ASJ) AF: 0.000925 AC: 20 AN: 21622

East Asian (EAS) AF: 0.0147 AC: 514 AN: 34896

South Asian (SAS) AF: 0.00809 AC: 541 AN: 66906

European-Finnish (FIN) AF: 0.0114 AC: 551 AN: 48492

Middle Eastern (MID) AF: 0.0201 AC: 93 AN: 4634

European-Non Finnish (NFE) AF: 0.00115 AC: 800 AN: 698600

Other (OTH) AF: 0.0182 AC: 790 AN: 43324

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

African (AFR) AF: 0.179 AC: 7449 AN: 41502

American (AMR) AF: 0.0237 AC: 363 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5184

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4828

European-Finnish (FIN) AF: 0.0111 AC: 118 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00172 AC: 117 AN: 68008

Other (OTH) AF: 0.0468 AC: 99 AN: 2116

Alfa AF: 0.0390 Hom.: 73

Bravo AF: 0.0604

Asia WGS AF: 0.0290 AC: 100 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	-0.75
CADD	Benign	7.8
DANN	Benign	0.52
PhyloP100		0.082
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: rs12241256; hg19: chr10-93699649;