rs4628973
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_027335.2(URAHP):n.228+1139T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,320 control chromosomes in the GnomAD database, including 18,370 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 0.46 ( 18370 hom., cov: 31)
Consequence
URAHP
NR_027335.2 intron, non_coding_transcript
NR_027335.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.91
Genes affected
URAHP (HGNC:43695): (urate (hydroxyiso-) hydrolase, pseudogene) Predicted to enable hydroxyisourate hydrolase activity. Predicted to be involved in allantoin metabolic process; purine-containing compound catabolic process; and urate catabolic process. Predicted to be active in peroxisome. [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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
URAHP | NR_027335.2 | n.228+1139T>C | intron_variant, non_coding_transcript_variant | |||||
URAHP | NR_027336.2 | n.181+1139T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
URAHP | ENST00000409873.5 | n.228+1139T>C | intron_variant, non_coding_transcript_variant | 1 | ||||||
URAHP | ENST00000517889.5 | n.171+1139T>C | intron_variant, non_coding_transcript_variant | 1 | ||||||
URAHP | ENST00000610227.1 | n.200+1139T>C | intron_variant, non_coding_transcript_variant | |||||||
URAHP | ENST00000521551.5 | n.234+1139T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.455 AC: 68841AN: 151202Hom.: 18316 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: 0.456 AC: 68955AN: 151320Hom.: 18370 Cov.: 31 AF XY: 0.464 AC XY: 34334AN XY: 73920
GnomAD4 genome
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2089
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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