Variant rs2071514 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001091.4(AOC1):c.1329G>A(p.Ala443Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,613,996 control chromosomes in the GnomAD database, including 40,209 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 0.21 ( 3920 hom., cov: 33)

Exomes 𝑓: 0.21 ( 36289 hom. )

Consequence

AOC1
NM_001091.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.50

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:

LOC105375567 (HGNC:):

LOC105375567 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP7

Synonymous conserved (PhyloP=-3.5 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AOC1	NM_001091.4 linkuse as main transcript	c.1329G>A	p.Ala443Ala	synonymous_variant	2/5	ENST00000360937.9	NP_001082.2	P19801-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AOC1	ENST00000360937.9 linkuse as main transcript	c.1329G>A	p.Ala443Ala	synonymous_variant	2/5	1	NM_001091.4	ENSP00000354193.4	P19801-1
AOC1	ENST00000416793.6 linkuse as main transcript	c.1329G>A	p.Ala443Ala	synonymous_variant	2/5	1		ENSP00000411613.2	P19801-2
AOC1	ENST00000467291.5 linkuse as main transcript	c.1329G>A	p.Ala443Ala	synonymous_variant	4/7	5		ENSP00000418328.1	P19801-1
AOC1	ENST00000493429.5 linkuse as main transcript	c.1329G>A	p.Ala443Ala	synonymous_variant	4/7	5		ENSP00000418614.1	P19801-1

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32676

AN:

152046

Hom.:

3914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.469

Gnomad SAS

AF:

0.344

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.208

GnomAD3 exomes

AF:

0.254

AC:

63455

AN:

249430

Hom.:

9483

AF XY:

0.253

AC XY:

34193

AN XY:

135326

show subpopulations

Gnomad AFR exome

AF:

0.201

Gnomad AMR exome

AF:

0.359

Gnomad ASJ exome

AF:

0.289

Gnomad EAS exome

AF:

0.461

Gnomad SAS exome

AF:

0.346

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.180

Gnomad OTH exome

AF:

0.228

GnomAD4 exome

AF:

0.207

AC:

303104

AN:

1461832

Hom.:

36289

Cov.:

AF XY:

0.211

AC XY:

153802

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.351

Gnomad4 ASJ exome

AF:

0.290

Gnomad4 EAS exome

AF:

0.508

Gnomad4 SAS exome

AF:

0.345

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.222

GnomAD4 genome

AF:

0.215

AC:

32701

AN:

152164

Hom.:

3920

Cov.:

AF XY:

0.220

AC XY:

16387

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.203

Gnomad4 AMR

AF:

0.277

Gnomad4 ASJ

AF:

0.296

Gnomad4 EAS

AF:

0.468

Gnomad4 SAS

AF:

0.343

Gnomad4 FIN

AF:

0.206

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.210

Alfa

AF:

0.198

Hom.:

4250

Bravo

AF:

0.221

Asia WGS

AF:

0.372

AC:

1289

AN:

3478

EpiCase

AF:

0.182

EpiControl

AF:

0.179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.46

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over