rs2302615
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002539.3(ODC1):c.-128+109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 153,462 control chromosomes in the GnomAD database, including 7,927 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.31 ( 7859 hom., cov: 35)
Exomes 𝑓: 0.29 ( 68 hom. )
Consequence
ODC1
NM_002539.3 intron
NM_002539.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.370
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 2-10448012-C-T is Benign according to our data. Variant chr2-10448012-C-T is described in ClinVar as [Benign]. Clinvar id is 13806.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODC1 | NM_002539.3 | c.-128+109G>A | intron_variant | ENST00000234111.9 | |||
ODC1 | NM_001287189.2 | c.-666G>A | 5_prime_UTR_variant | 1/12 | |||
ODC1 | NM_001287190.2 | c.-512G>A | 5_prime_UTR_variant | 1/12 | |||
ODC1 | NM_001287188.2 | c.-415+109G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODC1 | ENST00000234111.9 | c.-128+109G>A | intron_variant | 1 | NM_002539.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.312 AC: 47412AN: 151864Hom.: 7856 Cov.: 35
GnomAD3 genomes
?
AF:
AC:
47412
AN:
151864
Hom.:
Cov.:
35
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.291 AC: 433AN: 1490Hom.: 68 AF XY: 0.280 AC XY: 246AN XY: 880
GnomAD4 exome
AF:
AC:
433
AN:
1490
Hom.:
AF XY:
AC XY:
246
AN XY:
880
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.312 AC: 47454AN: 151972Hom.: 7859 Cov.: 35 AF XY: 0.322 AC XY: 23910AN XY: 74308
GnomAD4 genome
?
AF:
AC:
47454
AN:
151972
Hom.:
Cov.:
35
AF XY:
AC XY:
23910
AN XY:
74308
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1624
AN:
3450
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Ornithine decarboxylase 1 polymorphism Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jun 24, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at