dbSNP rs2071517: AOC1:c.*102G>A (chr7-150861311-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 NM_001091.4(AOC1):c.*102G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,364,082 control chromosomes in the GnomAD database, including 34,006 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 0.23 ( 4413 hom., cov: 32)

Exomes 𝑓: 0.21 ( 29593 hom. )

Consequence

AOC1
NM_001091.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.746

Publications

11 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOC1	NM_001091.4 link	c.*102G>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000360937.9	NP_001082.2	P19801-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000360937.9 link	c.*102G>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_001091.4	ENSP00000354193.4		P19801-1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34748

AN:

151910

Hom.:

4408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.222

GnomAD4 exome

AF:

0.206

AC:

249924

AN:

1212052

Hom.:

29593

Cov.:

AF XY:

0.210

AC XY:

123995

AN XY:

589398

show subpopulations

African (AFR)

AF:

0.238

AC:

6388

AN:

26800

American (AMR)

AF:

0.325

AC:

6528

AN:

20098

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

5391

AN:

18316

East Asian (EAS)

AF:

0.521

AC:

18041

AN:

34634

South Asian (SAS)

AF:

0.353

AC:

21039

AN:

59564

European-Finnish (FIN)

AF:

0.202

AC:

9029

AN:

44794

Middle Eastern (MID)

AF:

0.188

AC:

949

AN:

5040

European-Non Finnish (NFE)

AF:

0.180

AC:

170993

AN:

951894

Other (OTH)

AF:

0.227

AC:

11566

AN:

50912

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9533

19066

28598

38131

47664

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6456

12912

19368

25824

32280

<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:

0.229

AC:

34770

AN:

152030

Hom.:

4413

Cov.:

AF XY:

0.234

AC XY:

17357

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.241

AC:

9983

AN:

41484

American (AMR)

AF:

0.291

AC:

4445

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

1043

AN:

3472

East Asian (EAS)

AF:

0.484

AC:

2496

AN:

5160

South Asian (SAS)

AF:

0.349

AC:

1679

AN:

4814

European-Finnish (FIN)

AF:

0.207

AC:

2182

AN:

10558

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12272

AN:

67958

Other (OTH)

AF:

0.223

AC:

469

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1378

2757

4135

5514

6892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.200

Hom.:

5596

Bravo

AF:

0.237

Asia WGS

AF:

0.378

AC:

1308

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.6

(source)

DANN

Benign

0.58

PhyloP100

-0.75

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