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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001091.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC1	NM_001091.4	MANE Select	c.*102G>A		3_prime_UTR	Exon 5 of 5	NP_001082.2	P19801-1
	AOC1	NM_001272072.2		c.*102G>A		3_prime_UTR	Exon 5 of 5	NP_001259001.1	P19801-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AOC1	ENST00000360937.9	TSL:1 MANE Select	c.*102G>A	3_prime_UTR	Exon 5 of 5	ENSP00000354193.4	P19801-1
AOC1	ENST00000467291.5	TSL:5	c.*102G>A	3_prime_UTR	Exon 7 of 7	ENSP00000418328.1	P19801-1
AOC1	ENST00000493429.5	TSL:5	c.*102G>A	3_prime_UTR	Exon 7 of 7	ENSP00000418614.1	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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over