Genetic Variant ODC1:c.-166G>C (chr2-10448426-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

Publications

6 publications found

Variant links:

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 links:

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

ODC1-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
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.:

show subpopulations

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.:

AF XY:

0.562

AC XY:

27306

AN XY:

48610

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

769

1538

2308

3077

3846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

150

300

450

600

750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.645

AC:

95668

AN:

148216

Hom.:

31624

Cov.:

AF XY:

0.649

AC XY:

46854

AN XY:

72218

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1752

3505

5257

7010

8762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.58

PhyloP100

0.11

PromoterAI

0.064

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over