Variant 2-10440841-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

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

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

ODC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

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_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.41 with no splicing effect.

BA1

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	Protein
ODC1	NM_002539.3 linkuse as main transcript	c.1269C>T	p.Pro423=	synonymous_variant	12/12	ENST00000234111.9	NP_002530.1
ODC1	NM_001287189.2 linkuse as main transcript	c.1269C>T	p.Pro423=	synonymous_variant	12/12		NP_001274118.1
ODC1	NM_001287190.2 linkuse as main transcript	c.1269C>T	p.Pro423=	synonymous_variant	12/12		NP_001274119.1
ODC1	NM_001287188.2 linkuse as main transcript	c.882C>T	p.Pro294=	synonymous_variant	12/12		NP_001274117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODC1	ENST00000234111.9 linkuse as main transcript	c.1269C>T	p.Pro423=	synonymous_variant	12/12	1	NM_002539.3	ENSP00000234111	P1

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20464

AN:

151928

Hom.:

2477

Cov.:

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.:

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

AF:

0.135

AC:

20497

AN:

152046

Hom.:

2481

Cov.:

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over