Genetic Variant AOC1:c.-92-231G>T (chr7-150851884-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000941409.1(AOC1):c.-92-231G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,156 control chromosomes in the GnomAD database, including 4,356 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 ( 4353 hom., cov: 32)

Exomes 𝑓: 0.29 ( 3 hom. )

Consequence

AOC1
ENST00000941409.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.935

Publications

25 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:

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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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000941409.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
AOC1	ENST00000941409.1		c.-92-231G>T	intron	N/A	ENSP00000611468.1
AOC1	ENST00000467291.5	TSL:5	c.-92-231G>T	intron	N/A	ENSP00000418328.1
AOC1	ENST00000493429.5	TSL:5	c.-92-231G>T	intron	N/A	ENSP00000418614.1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35638

AN:

151914

Hom.:

4341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.223

GnomAD4 exome

AF:

0.290

AC:

AN:

124

Hom.:

AF XY:

0.298

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.271

AC:

AN:

Other (OTH)

AF:

0.286

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.528

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:

0.235

AC:

35668

AN:

152032

Hom.:

4353

Cov.:

AF XY:

0.232

AC XY:

17239

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.264

AC:

10943

AN:

41440

American (AMR)

AF:

0.182

AC:

2784

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

800

AN:

3470

East Asian (EAS)

AF:

0.120

AC:

618

AN:

5166

South Asian (SAS)

AF:

0.154

AC:

744

AN:

4830

European-Finnish (FIN)

AF:

0.260

AC:

2749

AN:

10564

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16274

AN:

67964

Other (OTH)

AF:

0.220

AC:

464

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1380

2760

4139

5519

6899

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.235

Hom.:

16268

Bravo

AF:

0.233

Asia WGS

AF:

0.147

AC:

514

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.069

(source)

DANN

Benign

0.59

PhyloP100

-0.94

PromoterAI

0.0013

Neutral

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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