Genetic Variant ODC1:c.-39A>G (chr2-10445176-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002539.3(ODC1):c.-39A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 590,594 control chromosomes in the GnomAD database, including 3,535 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 0.091 ( 822 hom., cov: 33)

Exomes 𝑓: 0.10 ( 2713 hom. )

Consequence

ODC1
NM_002539.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

Publications

9 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 Gene-Disease associations (from GenCC):

neurodevelopmental disorder with alopecia and brain abnormalities
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ODC1 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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ODC1	NM_002539.3 link	c.-39A>G	5_prime_UTR_variant	Exon 2 of 12	ENST00000234111.9	NP_002530.1	P11926
ODC1	NM_001287189.2 link	c.-39A>G	5_prime_UTR_variant	Exon 2 of 12		NP_001274118.1	P11926
ODC1	NM_001287190.2 link	c.-39A>G	5_prime_UTR_variant	Exon 2 of 12		NP_001274119.1	P11926
ODC1	NM_001287188.2 link	c.-326A>G	5_prime_UTR_variant	Exon 2 of 12		NP_001274117.1	B4DXF8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODC1	ENST00000234111.9 link	c.-39A>G		5_prime_UTR_variant	Exon 2 of 12	1	NM_002539.3	ENSP00000234111.4		P11926

Frequencies

GnomAD3 genomes

AF:

0.0912

AC:

13880

AN:

152142

Hom.:

822

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0458

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.0818

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0882

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0917

Gnomad OTH

AF:

0.0889

GnomAD4 exome

AF:

0.102

AC:

44858

AN:

438334

Hom.:

2713

Cov.:

AF XY:

0.102

AC XY:

23747

AN XY:

232854

show subpopulations

African (AFR)

AF:

0.0444

AC:

531

AN:

11966

American (AMR)

AF:

0.218

AC:

3996

AN:

18346

Ashkenazi Jewish (ASJ)

AF:

0.0852

AC:

1146

AN:

13450

East Asian (EAS)

AF:

0.181

AC:

5292

AN:

29304

South Asian (SAS)

AF:

0.101

AC:

4542

AN:

44942

European-Finnish (FIN)

AF:

0.0896

AC:

2586

AN:

28854

Middle Eastern (MID)

AF:

0.0456

AC:

101

AN:

2214

European-Non Finnish (NFE)

AF:

0.0913

AC:

24136

AN:

264304

Other (OTH)

AF:

0.101

AC:

2528

AN:

24954

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1832

3664

5495

7327

9159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

216

432

648

864

1080

<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:

0.0912

AC:

13888

AN:

152260

Hom.:

822

Cov.:

AF XY:

0.0940

AC XY:

6999

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0456

AC:

1896

AN:

41544

American (AMR)

AF:

0.176

AC:

2685

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0818

AC:

284

AN:

3470

East Asian (EAS)

AF:

0.208

AC:

1076

AN:

5184

South Asian (SAS)

AF:

0.101

AC:

489

AN:

4828

European-Finnish (FIN)

AF:

0.0882

AC:

935

AN:

10598

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0918

AC:

6242

AN:

68018

Other (OTH)

AF:

0.0903

AC:

191

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

632

1264

1896

2528

3160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.0917

Hom.:

292

Bravo

AF:

0.0995

Asia WGS

AF:

0.170

AC:

590

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.6

(source)

DANN

Benign

0.75

PhyloP100

0.016

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over