rs17054831
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001014286.3(SUPT20H):c.166-90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,480,152 control chromosomes in the GnomAD database, including 2,556 homozygotes. 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 0.074 ( 1427 hom., cov: 32)
Exomes 𝑓: 0.0072 ( 1129 hom. )
Consequence
SUPT20H
NM_001014286.3 intron
NM_001014286.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.274
Genes affected
SUPT20H (HGNC:20596): (SPT20 homolog, SAGA complex component) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of gluconeogenesis and positive regulation of transcription by RNA polymerase II. Part of SAGA-type complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUPT20H | NM_001014286.3 | c.166-90T>C | intron_variant | ENST00000350612.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUPT20H | ENST00000350612.11 | c.166-90T>C | intron_variant | 1 | NM_001014286.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0740 AC: 11252AN: 152152Hom.: 1409 Cov.: 32
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GnomAD4 exome AF: 0.00719 AC: 9554AN: 1327882Hom.: 1129 AF XY: 0.00627 AC XY: 4145AN XY: 660964
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GnomAD4 genome AF: 0.0742 AC: 11302AN: 152270Hom.: 1427 Cov.: 32 AF XY: 0.0719 AC XY: 5354AN XY: 74472
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at