2-10448426-C-G

Variant names:

• chr2-10448426-C-G
• rs28742580
• NM_002539.3:c.-433G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002539.3(ODC1):​c.-433G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 239,864 control chromosomes in the GnomAD database, including 46,629 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 0.65 (31624 hom., cov: 34)
  • Exomes 𝑓: 0.56 (15005 hom.)
• Consequence: ODC1 NM_002539.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

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]

ODC1-DT (HGNC:54070): (ODC1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODC1	NM_002539.3	c.-433G>C		upstream_gene_variant		ENST00000234111.9	NP_002530.1
ODC1	NM_001287188.2	c.-720G>C		upstream_gene_variant			NP_001274117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODC1	ENST00000234111.9	c.-433G>C		upstream_gene_variant		1	NM_002539.3	ENSP00000234111.4
ODC1	ENST00000699836.1	c.-323G>C		upstream_gene_variant				ENSP00000514634.1
ODC1	ENST00000446285.6	n.-433G>C		upstream_gene_variant		5		ENSP00000514632.1
ODC1-DT	ENST00000690575.1	n.-228C>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.645 AC: 95571 AN: 148118 Hom.: 31576 Cov.: 34

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.577

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.603

GnomAD4 exome AF: 0.564 AC: 51646 AN: 91648 Hom.: 15005 Cov.: 0 AF XY: 0.562 AC XY: 27306 AN XY: 48610

Gnomad4 AFR exome AF: 0.706

Gnomad4 AMR exome AF: 0.416

Gnomad4 ASJ exome AF: 0.444

Gnomad4 EAS exome AF: 0.571

Gnomad4 SAS exome AF: 0.677

Gnomad4 FIN exome AF: 0.639

Gnomad4 NFE exome AF: 0.558

Gnomad4 OTH exome AF: 0.553

GnomAD4 genome AF: 0.645 AC: 95668 AN: 148216 Hom.: 31624 Cov.: 34 AF XY: 0.649 AC XY: 46854 AN XY: 72218

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.605

Alfa AF: 0.635 Hom.: 3853

Bravo AF: 0.632

Asia WGS AF: 0.630 AC: 1863 AN: 2956

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.58

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: rs28742580; hg19: chr2-10588552;