rs2071514

Variant names:

• chr7-150857799-G-A
• rs2071514
• NM_001091.4:c.1329G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50
• Publications: 22 publications found

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]

ENSG00000289052 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.1329G>A	p.Ala443Ala	synonymous	Exon 2 of 5	NP_001082.2	P19801-1
	AOC1	NM_001272072.2		c.1329G>A	p.Ala443Ala	synonymous	Exon 2 of 5	NP_001259001.1	P19801-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC1	ENST00000360937.9	TSL:1 MANE Select	c.1329G>A	p.Ala443Ala	synonymous	Exon 2 of 5	ENSP00000354193.4	P19801-1
	AOC1	ENST00000416793.6	TSL:1	c.1329G>A	p.Ala443Ala	synonymous	Exon 2 of 5	ENSP00000411613.2	P19801-2
	AOC1	ENST00000941409.1		c.1329G>A	p.Ala443Ala	synonymous	Exon 3 of 6	ENSP00000611468.1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32676 AN: 152046 Hom.: 3914 Cov.: 33

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

GnomAD2 exomes AF: 0.254 AC: 63455 AN: 249430 AF XY: 0.253

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 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.: 36 AF XY: 0.211 AC XY: 153802 AN XY: 727212

African (AFR) AF: 0.202 AC: 6748 AN: 33480

American (AMR) AF: 0.351 AC: 15699 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 7581 AN: 26136

East Asian (EAS) AF: 0.508 AC: 20175 AN: 39700

South Asian (SAS) AF: 0.345 AC: 29798 AN: 86256

European-Finnish (FIN) AF: 0.200 AC: 10665 AN: 53418

Middle Eastern (MID) AF: 0.191 AC: 1104 AN: 5768

European-Non Finnish (NFE) AF: 0.178 AC: 197955 AN: 1111958

Other (OTH) AF: 0.222 AC: 13379 AN: 60396

GnomAD4 genome AF: 0.215 AC: 32701 AN: 152164 Hom.: 3920 Cov.: 33 AF XY: 0.220 AC XY: 16387 AN XY: 74370

African (AFR) AF: 0.203 AC: 8417 AN: 41520

American (AMR) AF: 0.277 AC: 4241 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2417 AN: 5160

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2183 AN: 10588

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12122 AN: 67998

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.199 Hom.: 10529

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.54
PhyloP100		-3.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2071514; hg19: chr7-150554887; COSMIC: COSV62867562; COSMIC: COSV62867562;