dbSNP rs7608353: ODC1:c.-127-1400T>C (chr2-10446664-A-G) – 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.-127-1400T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 330,504 control chromosomes in the GnomAD database, including 2,100 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 0.10 ( 936 hom., cov: 33)

Exomes 𝑓: 0.10 ( 1164 hom. )

Consequence

ODC1
NM_002539.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.579

Publications

2 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:

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=-0.82).

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.-127-1400T>C		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.-127-1400T>C		intron_variant	Intron 1 of 11	1	NM_002539.3	ENSP00000234111.4		P11926

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15606

AN:

152096

Hom.:

936

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0839

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.184

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:

0.0918

Gnomad OTH

AF:

0.0976

GnomAD4 exome

AF:

0.104

AC:

18490

AN:

178290

Hom.:

1164

Cov.:

AF XY:

0.102

AC XY:

11014

AN XY:

107636

show subpopulations

African (AFR)

AF:

0.0861

AC:

146

AN:

1696

American (AMR)

AF:

0.239

AC:

1538

AN:

6448

Ashkenazi Jewish (ASJ)

AF:

0.0938

AC:

428

AN:

4562

East Asian (EAS)

AF:

0.228

AC:

605

AN:

2650

South Asian (SAS)

AF:

0.105

AC:

4128

AN:

39178

European-Finnish (FIN)

AF:

0.0963

AC:

825

AN:

8568

Middle Eastern (MID)

AF:

0.0453

AC:

AN:

1170

European-Non Finnish (NFE)

AF:

0.0940

AC:

9944

AN:

105750

Other (OTH)

AF:

0.0995

AC:

823

AN:

8268

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

711

1422

2132

2843

3554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

148

222

296

370

<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:

0.103

AC:

15629

AN:

152214

Hom.:

936

Cov.:

AF XY:

0.105

AC XY:

7836

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0840

AC:

3488

AN:

41530

American (AMR)

AF:

0.184

AC:

2809

AN:

15284

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:

4832

European-Finnish (FIN)

AF:

0.0880

AC:

933

AN:

10600

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0918

AC:

6241

AN:

67998

Other (OTH)

AF:

0.0990

AC:

209

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

728

1456

2183

2911

3639

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.0941

Hom.:

119

Bravo

AF:

0.113

Asia WGS

AF:

0.172

AC:

598

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.9

(source)

DANN

Benign

0.57

PhyloP100

0.58

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