Genetic Variant ENST00000553181.6:n.1594-950G>C (chr2-10451331-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000553181.6(ODC1-DT):n.1594-950G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,544 control chromosomes in the GnomAD database, including 25,963 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 0.58 ( 25957 hom., cov: 29)

Exomes 𝑓: 0.81 ( 6 hom. )

Consequence

ODC1-DT
ENST00000553181.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243

Publications

1 publications found

Variant links:

Genes affected

ODC1-DT (HGNC:54070): (ODC1 divergent transcript)

ODC1-DT 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODC1-DT	NR_110597.1 link	n.374-950G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ODC1-DT	ENST00000553181.6 link	n.1594-950G>C	intron_variant	Intron 1 of 3	5
ODC1-DT	ENST00000667698.2 link	n.104-950G>C	intron_variant	Intron 1 of 3
ODC1-DT	ENST00000810589.1 link	n.899-950G>C	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

87861

AN:

151410

Hom.:

25927

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.453

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.652

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.544

GnomAD4 exome

AF:

0.813

AC:

AN:

Hom.:

Cov.:

AF XY:

0.875

AC XY:

AN XY:

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.580

AC:

87933

AN:

151528

Hom.:

25957

Cov.:

AF XY:

0.583

AC XY:

43156

AN XY:

74026

show subpopulations

African (AFR)

AF:

0.654

AC:

26997

AN:

41256

American (AMR)

AF:

0.521

AC:

7940

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.453

AC:

1572

AN:

3470

East Asian (EAS)

AF:

0.360

AC:

1852

AN:

5140

South Asian (SAS)

AF:

0.641

AC:

3084

AN:

4814

European-Finnish (FIN)

AF:

0.652

AC:

6820

AN:

10458

Middle Eastern (MID)

AF:

0.521

AC:

152

AN:

292

European-Non Finnish (NFE)

AF:

0.556

AC:

37760

AN:

67856

Other (OTH)

AF:

0.550

AC:

1154

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1779

3559

5338

7118

8897

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

750

1500

2250

3000

3750

<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:

0.451

Hom.:

1224

Bravo

AF:

0.571

Asia WGS

AF:

0.537

AC:

1869

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.67

(source)

DANN

Benign

0.38

PhyloP100

-0.24

Mutation Taster

=100/0

polymorphism

(source)

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