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2-10440841-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_002539.3(ODC1):c.1269C>T(p.Pro423=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 1,613,840 control chromosomes in the GnomAD database, including 13,821 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 2481 hom., cov: 32)
Exomes 𝑓: 0.075 ( 11340 hom. )

Consequence

ODC1
NM_002539.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.41
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-10440841-G-A is Benign according to our data. Variant chr2-10440841-G-A is described in ClinVar as [Benign]. Clinvar id is 1280616.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.41 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ODC1NM_002539.3 linkuse as main transcriptc.1269C>T p.Pro423= synonymous_variant 12/12 ENST00000234111.9
ODC1NM_001287189.2 linkuse as main transcriptc.1269C>T p.Pro423= synonymous_variant 12/12
ODC1NM_001287190.2 linkuse as main transcriptc.1269C>T p.Pro423= synonymous_variant 12/12
ODC1NM_001287188.2 linkuse as main transcriptc.882C>T p.Pro294= synonymous_variant 12/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ODC1ENST00000234111.9 linkuse as main transcriptc.1269C>T p.Pro423= synonymous_variant 12/121 NM_002539.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.135
AC:
20464
AN:
151928
Hom.:
2477
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.250
Gnomad AMI
AF:
0.00440
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.0456
Gnomad EAS
AF:
0.541
Gnomad SAS
AF:
0.234
Gnomad FIN
AF:
0.121
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.0393
Gnomad OTH
AF:
0.108
GnomAD3 exomes
AF:
0.135
AC:
34020
AN:
251400
Hom.:
4766
AF XY:
0.132
AC XY:
17891
AN XY:
135890
show subpopulations
Gnomad AFR exome
AF:
0.258
Gnomad AMR exome
AF:
0.136
Gnomad ASJ exome
AF:
0.0461
Gnomad EAS exome
AF:
0.549
Gnomad SAS exome
AF:
0.215
Gnomad FIN exome
AF:
0.119
Gnomad NFE exome
AF:
0.0421
Gnomad OTH exome
AF:
0.0976
GnomAD4 exome
AF:
0.0748
AC:
109383
AN:
1461794
Hom.:
11340
Cov.:
31
AF XY:
0.0779
AC XY:
56668
AN XY:
727194
show subpopulations
Gnomad4 AFR exome
AF:
0.255
Gnomad4 AMR exome
AF:
0.133
Gnomad4 ASJ exome
AF:
0.0464
Gnomad4 EAS exome
AF:
0.546
Gnomad4 SAS exome
AF:
0.213
Gnomad4 FIN exome
AF:
0.112
Gnomad4 NFE exome
AF:
0.0370
Gnomad4 OTH exome
AF:
0.100
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.135
AC:
20497
AN:
152046
Hom.:
2481
Cov.:
32
AF XY:
0.142
AC XY:
10574
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.250
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.0456
Gnomad4 EAS
AF:
0.541
Gnomad4 SAS
AF:
0.233
Gnomad4 FIN
AF:
0.121
Gnomad4 NFE
AF:
0.0393
Gnomad4 OTH
AF:
0.112
Alfa
AF:
0.0595
Hom.:
1281
Bravo
AF:
0.140
Asia WGS
AF:
0.357
AC:
1241
AN:
3478
EpiCase
AF:
0.0398
EpiControl
AF:
0.0406

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 22, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
3.6
Dann
Benign
0.69

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1049500; hg19: chr2-10580967; COSMIC: COSV52171477; COSMIC: COSV52171477; API