Genetic Variant ENSG00000298698:n.252-3787G>A (chr2-10439895-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000757451.1(ENSG00000298698):n.252-3787G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,582 control chromosomes in the GnomAD database, including 801 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 0.090 ( 801 hom., cov: 32)

Exomes 𝑓: 0.073 ( 0 hom. )

Consequence

ENSG00000298698
ENST00000757451.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435

Publications

2 publications found

Variant links:

Genes affected

ENSG00000298698 (HGNC:):

ENSG00000298698 links:

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ODC1	NM_002539.3 link	c.*829C>T	downstream_gene_variant	ENST00000234111.9	NP_002530.1	P11926
ODC1	NM_001287189.2 link	c.*829C>T	downstream_gene_variant		NP_001274118.1	P11926
ODC1	NM_001287190.2 link	c.*829C>T	downstream_gene_variant		NP_001274119.1	P11926
ODC1	NM_001287188.2 link	c.*829C>T	downstream_gene_variant		NP_001274117.1	B4DXF8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000298698	ENST00000757451.1 link	n.252-3787G>A	intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1 link	n.133-1547G>A	intron_variant	Intron 1 of 2
ODC1	ENST00000234111.9 link	c.*829C>T	downstream_gene_variant		1	NM_002539.3	ENSP00000234111.4	P11926
ODC1	ENST00000446285.6 link	n.*1983C>T	downstream_gene_variant		5		ENSP00000514632.1	A0A8V8TQA2

Frequencies

GnomAD3 genomes

AF:

0.0897

AC:

13650

AN:

152106

Hom.:

801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0455

Gnomad AMI

AF:

0.0384

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.0808

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0876

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0900

Gnomad OTH

AF:

0.0864

GnomAD4 exome

AF:

0.0726

AC:

AN:

358

Hom.:

AF XY:

0.0720

AC XY:

AN XY:

250

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.100

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.0833

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0700

AC:

AN:

300

Other (OTH)

AF:

0.111

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0897

AC:

13657

AN:

152224

Hom.:

801

Cov.:

AF XY:

0.0926

AC XY:

6891

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0453

AC:

1883

AN:

41540

American (AMR)

AF:

0.175

AC:

2672

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0808

AC:

280

AN:

3466

East Asian (EAS)

AF:

0.204

AC:

1056

AN:

5176

South Asian (SAS)

AF:

0.101

AC:

486

AN:

4818

European-Finnish (FIN)

AF:

0.0876

AC:

929

AN:

10606

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0900

AC:

6120

AN:

68004

Other (OTH)

AF:

0.0879

AC:

186

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

643

1287

1930

2574

3217

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:

0.0840

Hom.:

Bravo

AF:

0.0977

Asia WGS

AF:

0.167

AC:

579

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.4

(source)

DANN

Benign

0.79

PhyloP100

-0.43

Splicing

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