ENST00000887503.1:c.-166G>C

Variant names:

• chr2-10448426-C-G
• rs28742580
• ENST00000887503.1:c.-166G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000887503.1(ODC1):​c.-166G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 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 ENST00000887503.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000887503.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODC1	NM_002539.3	MANE Select	c.-433G>C		upstream_gene	N/A	NP_002530.1	P11926
	ODC1	NM_001287188.2		c.-720G>C		upstream_gene	N/A	NP_001274117.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODC1	ENST00000887503.1		c.-166G>C		5_prime_UTR	Exon 1 of 12	ENSP00000557562.1
	ODC1	ENST00000926727.1		c.-508G>C		5_prime_UTR	Exon 1 of 13	ENSP00000596786.1
	ODC1	ENST00000887501.1		c.-128+1342G>C		intron	N/A	ENSP00000557560.1

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

African (AFR) AF: 0.706 AC: 1284 AN: 1818

American (AMR) AF: 0.416 AC: 1121 AN: 2692

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1268 AN: 2854

East Asian (EAS) AF: 0.571 AC: 4939 AN: 8646

South Asian (SAS) AF: 0.677 AC: 1083 AN: 1600

European-Finnish (FIN) AF: 0.639 AC: 5518 AN: 8638

Middle Eastern (MID) AF: 0.530 AC: 250 AN: 472

European-Non Finnish (NFE) AF: 0.558 AC: 33246 AN: 59614

Other (OTH) AF: 0.553 AC: 2937 AN: 5314

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

African (AFR) AF: 0.764 AC: 31456 AN: 41164

American (AMR) AF: 0.499 AC: 7466 AN: 14956

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1674 AN: 3396

East Asian (EAS) AF: 0.633 AC: 3195 AN: 5048

South Asian (SAS) AF: 0.704 AC: 3388 AN: 4812

European-Finnish (FIN) AF: 0.713 AC: 6650 AN: 9332

Middle Eastern (MID) AF: 0.579 AC: 168 AN: 290

European-Non Finnish (NFE) AF: 0.601 AC: 39819 AN: 66248

Other (OTH) AF: 0.605 AC: 1247 AN: 2062

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		0.11
PromoterAI		0.064	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs28742580; hg19: chr2-10588552;