rs2302614
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002539.3(ODC1):c.-48T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 574,910 control chromosomes in the GnomAD database, including 8,751 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 0.13 ( 2310 hom., cov: 33)
Exomes 𝑓: 0.11 ( 6441 hom. )
Consequence
ODC1
NM_002539.3 5_prime_UTR
NM_002539.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.35
Genes affected
ODC1 (HGNC:8109): (ornithine decarboxylase 1) This gene encodes the rate-limiting enzyme of the polyamine biosynthesis pathway which catalyzes ornithine to putrescine. The activity level for the enzyme varies in response to growth-promoting stimuli and exhibits a high turnover rate in comparison to other mammalian proteins. Originally localized to both chromosomes 2 and 7, the gene encoding this enzyme has been determined to be located on 2p25, with a pseudogene located on 7q31-qter. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Dec 2013]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODC1 | NM_002539.3 | c.-48T>G | 5_prime_UTR_variant | 2/12 | ENST00000234111.9 | ||
ODC1 | NM_001287188.2 | c.-335T>G | 5_prime_UTR_variant | 2/12 | |||
ODC1 | NM_001287189.2 | c.-48T>G | 5_prime_UTR_variant | 2/12 | |||
ODC1 | NM_001287190.2 | c.-48T>G | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODC1 | ENST00000234111.9 | c.-48T>G | 5_prime_UTR_variant | 2/12 | 1 | NM_002539.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.130 AC: 19789AN: 152144Hom.: 2306 Cov.: 33
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GnomAD4 exome AF: 0.111 AC: 46737AN: 422648Hom.: 6441 Cov.: 4 AF XY: 0.114 AC XY: 25566AN XY: 224534
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GnomAD4 genome ? AF: 0.130 AC: 19821AN: 152262Hom.: 2310 Cov.: 33 AF XY: 0.138 AC XY: 10283AN XY: 74454
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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