rs1023021
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000437147.8(TAF1):c.1361-20454A>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.69 ( 13885 hom., 6293 hem., cov: 11)
Failed GnomAD Quality Control
Consequence
TAF1
ENST00000437147.8 intron, NMD_transcript
ENST00000437147.8 intron, NMD_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.07
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.06).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF1 | NR_104387.2 | n.5520-20454A>C | intron_variant, non_coding_transcript_variant | ||||
TAF1 | NR_104388.2 | n.5511-20454A>C | intron_variant, non_coding_transcript_variant | ||||
TAF1 | NR_104389.2 | n.5418-20454A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF1 | ENST00000437147.8 | c.1361-20454A>C | intron_variant, NMD_transcript_variant | 1 | |||||
TAF1 | ENST00000462588.5 | c.1000-20454A>C | intron_variant, NMD_transcript_variant | 1 | |||||
TAF1 | ENST00000467309.5 | c.*107-20454A>C | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.687 AC: 48867AN: 71145Hom.: 13887 Cov.: 11 AF XY: 0.616 AC XY: 6297AN XY: 10229
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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: InbreedingCoeff AF: 0.687 AC: 48848AN: 71117Hom.: 13885 Cov.: 11 AF XY: 0.615 AC XY: 6293AN XY: 10229
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at