dbSNP rs2302615: ODC1:c.-128+109G>A (chr2-10448012-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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 (★).

Frequency

Genomes: 𝑓 0.31 ( 7859 hom., cov: 35)

Exomes 𝑓: 0.29 ( 68 hom. )

Consequence

ODC1
NM_002539.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.370

Publications

19 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 -14 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 VariationId is 13806.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
ODC1	NM_002539.3 link	c.-128+109G>A	intron_variant	Intron 1 of 11	ENST00000234111.9	NP_002530.1
ODC1	NM_001287189.2 link	c.-666G>A	5_prime_UTR_variant	Exon 1 of 12		NP_001274118.1
ODC1	NM_001287190.2 link	c.-512G>A	5_prime_UTR_variant	Exon 1 of 12		NP_001274119.1
ODC1	NM_001287188.2 link	c.-415+109G>A	intron_variant	Intron 1 of 11		NP_001274117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODC1	ENST00000234111.9 link	c.-128+109G>A		intron_variant	Intron 1 of 11	1	NM_002539.3	ENSP00000234111.4

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47412

AN:

151864

Hom.:

7856

Cov.:

show subpopulations

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.:

AF XY:

0.280

AC XY:

246

AN XY:

880

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AF:

0.271

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

AN:

East Asian (EAS)

AF:

0.688

AC:

AN:

South Asian (SAS)

AF:

0.300

AC:

AN:

European-Finnish (FIN)

AF:

0.359

AC:

AN:

192

Middle Eastern (MID)

AF:

0.300

AC:

AN:

European-Non Finnish (NFE)

AF:

0.259

AC:

262

AN:

1010

Other (OTH)

AF:

0.293

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.312

AC:

47454

AN:

151972

Hom.:

7859

Cov.:

AF XY:

0.322

AC XY:

23910

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.376

AC:

15607

AN:

41482

American (AMR)

AF:

0.262

AC:

4001

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

750

AN:

3466

East Asian (EAS)

AF:

0.561

AC:

2882

AN:

5134

South Asian (SAS)

AF:

0.421

AC:

2034

AN:

4832

European-Finnish (FIN)

AF:

0.390

AC:

4122

AN:

10556

Middle Eastern (MID)

AF:

0.257

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.254

AC:

17233

AN:

67904

Other (OTH)

AF:

0.292

AC:

617

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1737

3475

5212

6950

8687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.294

Hom.:

816

Bravo

AF:

0.307

Asia WGS

AF:

0.471

AC:

1624

AN:

3450

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Ornithine decarboxylase 1 polymorphism

Benign:1

Jun 24, 2003

OMIM

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.97

PhyloP100

0.37

PromoterAI

-0.086

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over