chr10-91942648-C-T

Variant names:

• chr10-91942648-C-T
• rs3814640
• NM_003972.3:c.400+80C>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.400+80C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,440,926 control chromosomes in the GnomAD database, including 103,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.32 (8889 hom., cov: 31)
  • Exomes 𝑓: 0.38 (94433 hom.)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.318
• Publications: 3 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 10-91942648-C-T is Benign according to our data. Variant chr10-91942648-C-T is described in ClinVar as Benign. ClinVar VariationId is 1234034.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 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.400+80C>T		intron	N/A	NP_003963.1	Q2M1V9
	BTAF1	NR_165090.1		n.707+80C>T		intron	N/A
	BTAF1	NR_165091.1		n.707+80C>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.400+80C>T		intron	N/A	ENSP00000265990.6	O14981-1
	BTAF1	ENST00000928671.1		c.400+80C>T		intron	N/A	ENSP00000598730.1
	BTAF1	ENST00000928669.1		c.253+2582C>T		intron	N/A	ENSP00000598728.1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48506 AN: 151898 Hom.: 8874 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.379 AC: 487960 AN: 1288910 Hom.: 94433 AF XY: 0.381 AC XY: 244213 AN XY: 640660

African (AFR) AF: 0.134 AC: 3903 AN: 29146

American (AMR) AF: 0.472 AC: 17172 AN: 36362

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 7410 AN: 21972

East Asian (EAS) AF: 0.491 AC: 18766 AN: 38218

South Asian (SAS) AF: 0.505 AC: 36568 AN: 72412

European-Finnish (FIN) AF: 0.462 AC: 22426 AN: 48504

Middle Eastern (MID) AF: 0.296 AC: 1555 AN: 5260

European-Non Finnish (NFE) AF: 0.366 AC: 360193 AN: 983062

Other (OTH) AF: 0.370 AC: 19967 AN: 53974

GnomAD4 genome AF: 0.319 AC: 48544 AN: 152016 Hom.: 8889 Cov.: 31 AF XY: 0.331 AC XY: 24587 AN XY: 74260

African (AFR) AF: 0.146 AC: 6057 AN: 41494

American (AMR) AF: 0.394 AC: 6005 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2572 AN: 5152

South Asian (SAS) AF: 0.522 AC: 2516 AN: 4816

European-Finnish (FIN) AF: 0.466 AC: 4918 AN: 10546

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24302 AN: 67974

Other (OTH) AF: 0.301 AC: 633 AN: 2106

Alfa AF: 0.329 Hom.: 3408

Bravo AF: 0.301

Asia WGS AF: 0.499 AC: 1732 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	4.0
DANN	Benign	0.67
PhyloP100		-0.32
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		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: rs3814640; hg19: chr10-93702405; COSMIC: COSV56431265;