rs117704022

Variant names:

• chr10-91951243-T-A
• rs117704022
• NM_003972.3:c.401-160T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-91951243-T-A
• chr10-91951243-T-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003972.3(BTAF1):​c.401-160T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 152,312 control chromosomes in the GnomAD database, including 359 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.059 (359 hom., cov: 31)
• Consequence: BTAF1 NM_003972.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.17
• 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP6: Variant 10-91951243-T-A is Benign according to our data. Variant chr10-91951243-T-A is described in ClinVar as Benign. ClinVar VariationId is 1247960.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0875 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.401-160T>A		intron	N/A	NP_003963.1	Q2M1V9
	BTAF1	NR_165090.1		n.708-160T>A		intron	N/A
	BTAF1	NR_165091.1		n.708-160T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTAF1	ENST00000265990.12	TSL:1 MANE Select	c.401-160T>A		intron	N/A	ENSP00000265990.6	O14981-1
	BTAF1	ENST00000928671.1		c.401-160T>A		intron	N/A	ENSP00000598730.1
	BTAF1	ENST00000928669.1		c.254-160T>A		intron	N/A	ENSP00000598728.1

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8955 AN: 152194 Hom.: 360 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.0707

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0588 AC: 8950 AN: 152312 Hom.: 359 Cov.: 31 AF XY: 0.0564 AC XY: 4199 AN XY: 74490

African (AFR) AF: 0.0154 AC: 640 AN: 41580

American (AMR) AF: 0.0681 AC: 1042 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5196

South Asian (SAS) AF: 0.0215 AC: 104 AN: 4826

European-Finnish (FIN) AF: 0.0502 AC: 533 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6076 AN: 68006

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0426 Hom.: 33

Bravo AF: 0.0587

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		1.2
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: rs117704022; hg19: chr10-93711000;