dbSNP rs28362380: ODC1:c.-127-1390A>G (chr2-10446654-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.-127-1390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 307,362 control chromosomes in the GnomAD database, including 1,796 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 ( 806 hom., cov: 33)

Exomes 𝑓: 0.10 ( 990 hom. )

Consequence

ODC1
NM_002539.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

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:

SNORA80B (HGNC:34355): (small nucleolar RNA, H/ACA box 80B)

SNORA80B links:

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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=-0.86).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODC1	NM_002539.3 link	c.-127-1390A>G		intron_variant	Intron 1 of 11	ENST00000234111.9	NP_002530.1	P11926

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODC1	ENST00000234111.9 link	c.-127-1390A>G		intron_variant	Intron 1 of 11	1	NM_002539.3	ENSP00000234111.4		P11926

Frequencies

GnomAD3 genomes

AF:

0.0911

AC:

13864

AN:

152174

Hom.:

806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0457

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.0858

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0880

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0915

Gnomad OTH

AF:

0.0899

GnomAD4 exome

AF:

0.0999

AC:

15489

AN:

155070

Hom.:

990

AF XY:

0.0993

AC XY:

9300

AN XY:

93674

show subpopulations

African (AFR)

AF:

0.0421

AC:

AN:

1472

American (AMR)

AF:

0.217

AC:

1103

AN:

5090

Ashkenazi Jewish (ASJ)

AF:

0.0945

AC:

348

AN:

3684

East Asian (EAS)

AF:

0.221

AC:

448

AN:

2026

South Asian (SAS)

AF:

0.104

AC:

3621

AN:

34756

European-Finnish (FIN)

AF:

0.0956

AC:

695

AN:

7268

Middle Eastern (MID)

AF:

0.0370

AC:

AN:

838

European-Non Finnish (NFE)

AF:

0.0916

AC:

8492

AN:

92678

Other (OTH)

AF:

0.0949

AC:

689

AN:

7258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

595

1190

1784

2379

2974

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

150

200

250

<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:

0.0911

AC:

13872

AN:

152292

Hom.:

806

Cov.:

AF XY:

0.0939

AC XY:

6988

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0456

AC:

1896

AN:

41576

American (AMR)

AF:

0.175

AC:

2673

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0858

AC:

298

AN:

3472

East Asian (EAS)

AF:

0.207

AC:

1072

AN:

5180

South Asian (SAS)

AF:

0.101

AC:

489

AN:

4830

European-Finnish (FIN)

AF:

0.0880

AC:

934

AN:

10612

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0915

AC:

6227

AN:

68022

Other (OTH)

AF:

0.0913

AC:

193

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

656

1312

1968

2624

3280

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0861

Hom.:

106

Bravo

AF:

0.0995

Asia WGS

AF:

0.170

AC:

591

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.0

(source)

DANN

Benign

0.49

PhyloP100

-1.4

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

Computational scores

Splicing

Publications

Other links and lift over