dbSNP rs12179: AOC1:p.Ser630Ser (chr7-150860534-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001091.4(AOC1):c.1890G>A(p.Ser630Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,613,522 control chromosomes in the GnomAD database, including 93,764 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 0.37 ( 11231 hom., cov: 31)

Exomes 𝑓: 0.33 ( 82533 hom. )

Consequence

AOC1
NM_001091.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -7.58

Publications

23 publications found

Variant links:

Genes affected

AOC1 (HGNC:80): (amine oxidase copper containing 1) This gene encodes a metal-binding membrane glycoprotein that oxidatively deaminates putrescine, histamine, and related compounds. The encoded protein is inhibited by amiloride, a diuretic that acts by closing epithelial sodium ion channels. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]

AOC1 links:

ENSG00000289052 (HGNC:):

ENSG00000289052 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP7

Synonymous conserved (PhyloP=-7.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOC1	NM_001091.4 link	c.1890G>A	p.Ser630Ser	synonymous_variant	Exon 4 of 5	ENST00000360937.9	NP_001082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000360937.9 link	c.1890G>A	p.Ser630Ser	synonymous_variant	Exon 4 of 5	1	NM_001091.4	ENSP00000354193.4

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56553

AN:

151742

Hom.:

11223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.406

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.506

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.351

GnomAD2 exomes

AF:

0.370

AC:

92370

AN:

249364

AF XY:

0.369

show subpopulations

Gnomad AFR exome

AF:

0.478

Gnomad AMR exome

AF:

0.421

Gnomad ASJ exome

AF:

0.391

Gnomad EAS exome

AF:

0.502

Gnomad FIN exome

AF:

0.321

Gnomad NFE exome

AF:

0.296

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.326

AC:

476282

AN:

1461662

Hom.:

82533

Cov.:

AF XY:

0.330

AC XY:

239866

AN XY:

727136

show subpopulations

African (AFR)

AF:

0.481

AC:

16102

AN:

33480

American (AMR)

AF:

0.419

AC:

18736

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

10306

AN:

26134

East Asian (EAS)

AF:

0.536

AC:

21297

AN:

39700

South Asian (SAS)

AF:

0.490

AC:

42267

AN:

86252

European-Finnish (FIN)

AF:

0.317

AC:

16935

AN:

53374

Middle Eastern (MID)

AF:

0.295

AC:

1700

AN:

5768

European-Non Finnish (NFE)

AF:

0.295

AC:

328359

AN:

1111846

Other (OTH)

AF:

0.341

AC:

20580

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

18932

37864

56795

75727

94659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11180

22360

33540

44720

55900

<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:

0.373

AC:

56589

AN:

151860

Hom.:

11231

Cov.:

AF XY:

0.374

AC XY:

27779

AN XY:

74206

show subpopulations

African (AFR)

AF:

0.478

AC:

19808

AN:

41416

American (AMR)

AF:

0.378

AC:

5768

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1411

AN:

3466

East Asian (EAS)

AF:

0.505

AC:

2598

AN:

5142

South Asian (SAS)

AF:

0.494

AC:

2374

AN:

4804

European-Finnish (FIN)

AF:

0.317

AC:

3351

AN:

10580

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20079

AN:

67890

Other (OTH)

AF:

0.351

AC:

740

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1770

3540

5310

7080

8850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.325

Hom.:

21020

Bravo

AF:

0.381

Asia WGS

AF:

0.470

AC:

1632

AN:

3478

EpiCase

AF:

0.295

EpiControl

AF:

0.291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.049

(source)

DANN

Benign

0.73

PhyloP100

-7.6

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