Variant X-71431003-ATTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_004606.5(TAF1):c.4753+6794del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0067 ( 2 hom., 2 hem., cov: 15)

Failed GnomAD Quality Control

Consequence

TAF1
NM_004606.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

Variant links:

Genes affected

TAF1 (HGNC:11535): (TATA-box binding protein associated factor 1) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is the basal transcription factor TFIID, which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes the largest subunit of TFIID. This subunit binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation. This subunit contains two independent protein kinase domains at the N- and C-terminals, but also possesses acetyltransferase activity and can act as a ubiquitin-activating/conjugating enzyme. Mutations in this gene result in Dystonia 3, torsion, X-linked, a dystonia-parkinsonism disorder. Alternative splicing of this gene results in multiple transcript variants. This gene is part of a complex transcription unit (TAF1/DYT3), wherein some transcript variants share exons with TAF1 as well as additional downstream DYT3 exons. [provided by RefSeq, Oct 2013]

TAF1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF1	NM_004606.5 linkuse as main transcript	c.4753+6794del		intron_variant		ENST00000423759.6	NP_004597.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF1	ENST00000423759.6 linkuse as main transcript	c.4753+6794del		intron_variant		5	NM_004606.5	ENSP00000406549	A2

Frequencies

GnomAD3 genomes

AF:

0.00671

AC:

460

AN:

68593

Hom.:

Cov.:

AF XY:

0.000125

AC XY:

AN XY:

16033

show subpopulations

Gnomad AFR

AF:

0.0206

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00541

Gnomad ASJ

AF:

0.00319

Gnomad EAS

AF:

0.0132

Gnomad SAS

AF:

0.00129

Gnomad FIN

AF:

0.000797

Gnomad MID

AF:

0.0196

Gnomad NFE

AF:

0.00159

Gnomad OTH

AF:

0.00989

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00669

AC:

459

AN:

68587

Hom.:

Cov.:

AF XY:

0.000125

AC XY:

AN XY:

16031

show subpopulations

Gnomad4 AFR

AF:

0.0205

Gnomad4 AMR

AF:

0.00540

Gnomad4 ASJ

AF:

0.00319

Gnomad4 EAS

AF:

0.0132

Gnomad4 SAS

AF:

0.00130

Gnomad4 FIN

AF:

0.000797

Gnomad4 NFE

AF:

0.00159

Gnomad4 OTH

AF:

0.00983

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing