ENST00000454967.1:c.70-4847A>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000454967.1(SAMD13):c.70-4847A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,924 control chromosomes in the GnomAD database, including 14,973 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 0.42 ( 14973 hom., cov: 31)
Consequence
SAMD13
ENST00000454967.1 intron
ENST00000454967.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.152
Genes affected
SAMD13 (HGNC:24582): (sterile alpha motif domain containing 13) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
UOX (HGNC:12575): (urate oxidase (pseudogene)) Urate oxidase is an enzyme that catalyzes the oxidation of uric acid to allantoin. This gene has been inactivated by mutation and is nonfunctional in humans and some other primates. [provided by RefSeq, Jul 2008]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UOX | NR_003927.2 | n.209+1160T>A | intron_variant | Intron 1 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMD13 | ENST00000454967.1 | c.70-4847A>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000391978.1 | ||||
UOX | ENST00000471089.6 | n.249+1160T>A | intron_variant | Intron 2 of 7 | 6 | |||||
UOX | ENST00000483236.2 | n.209+1160T>A | intron_variant | Intron 1 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.423 AC: 64143AN: 151806Hom.: 14962 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.422 AC: 64167AN: 151924Hom.: 14973 Cov.: 31 AF XY: 0.421 AC XY: 31227AN XY: 74226
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3478
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