10-91951243-T-A

Position:

• chr10-91951243-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTAF1	NM_003972.3	c.401-160T>A		intron_variant		ENST00000265990.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTAF1	ENST00000265990.12	c.401-160T>A		intron_variant		1	NM_003972.3	P1

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

Gnomad4 AFR AF: 0.0154

Gnomad4 AMR AF: 0.0681

Gnomad4 ASJ AF: 0.0925

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0215

Gnomad4 FIN AF: 0.0502

Gnomad4 NFE AF: 0.0893

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0426 Hom.: 33

Bravo AF: 0.0587

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs117704022; hg19: chr10-93711000;