rs2302615

Positions:

• chr2-10448012-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

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
• Clinical Significance: Benign no assertion criteria provided B:1
• 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]

ACMG classification

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: 47412 AN: 151864 Hom.: 7856 Cov.: 35

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.291 AC: 433 AN: 1490 Hom.: 68 AF XY: 0.280 AC XY: 246 AN XY: 880

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.271

Gnomad4 ASJ exome AF: 0.237

Gnomad4 EAS exome AF: 0.688

Gnomad4 SAS exome AF: 0.300

Gnomad4 FIN exome AF: 0.359

Gnomad4 NFE exome AF: 0.259

Gnomad4 OTH exome AF: 0.293

GnomAD4 genome AF: 0.312 AC: 47454 AN: 151972 Hom.: 7859 Cov.: 35 AF XY: 0.322 AC XY: 23910 AN XY: 74308

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.292

Alfa AF: 0.294 Hom.: 816

Bravo AF: 0.307

Asia WGS AF: 0.471 AC: 1624 AN: 3450

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Ornithine decarboxylase 1 polymorphism Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jun 24, 2003

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.97
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2302615; hg19: chr2-10588138;