chr7-150860577-C-G

Variant names:

• chr7-150860577-C-G
• rs1049793
• NM_001091.4:c.1933C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001091.4(AOC1):​c.1933C>G​(p.His645Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,613,582 control chromosomes in the GnomAD database, including 93,694 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H645Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.37 (11216 hom., cov: 31)
  • Exomes 𝑓: 0.33 (82478 hom.)
• Consequence: AOC1 NM_001091.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 71 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=2.887249E-4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC1	NM_001091.4	MANE Select	c.1933C>G	p.His645Asp	missense	Exon 4 of 5	NP_001082.2
	AOC1	NM_001272072.2		c.1990C>G	p.His664Asp	missense	Exon 4 of 5	NP_001259001.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC1	ENST00000360937.9	TSL:1 MANE Select	c.1933C>G	p.His645Asp	missense	Exon 4 of 5	ENSP00000354193.4
	AOC1	ENST00000416793.6	TSL:1	c.1990C>G	p.His664Asp	missense	Exon 4 of 5	ENSP00000411613.2
	AOC1	ENST00000467291.5	TSL:5	c.1933C>G	p.His645Asp	missense	Exon 6 of 7	ENSP00000418328.1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56512 AN: 151786 Hom.: 11208 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.351

GnomAD2 exomes AF: 0.370 AC: 92361 AN: 249490 AF XY: 0.369

Gnomad AFR exome AF: 0.478

Gnomad AMR exome AF: 0.421

Gnomad ASJ exome AF: 0.391

Gnomad EAS exome AF: 0.502

Gnomad FIN exome AF: 0.320

Gnomad NFE exome AF: 0.296

Gnomad OTH exome AF: 0.337

GnomAD4 exome AF: 0.326 AC: 476088 AN: 1461678 Hom.: 82478 Cov.: 55 AF XY: 0.330 AC XY: 239760 AN XY: 727158

African (AFR) AF: 0.481 AC: 16096 AN: 33470

American (AMR) AF: 0.419 AC: 18733 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 10306 AN: 26134

East Asian (EAS) AF: 0.537 AC: 21300 AN: 39698

South Asian (SAS) AF: 0.490 AC: 42263 AN: 86244

European-Finnish (FIN) AF: 0.315 AC: 16842 AN: 53392

Middle Eastern (MID) AF: 0.295 AC: 1700 AN: 5768

European-Non Finnish (NFE) AF: 0.295 AC: 328280 AN: 1111854

Other (OTH) AF: 0.341 AC: 20568 AN: 60394

GnomAD4 genome AF: 0.372 AC: 56548 AN: 151904 Hom.: 11216 Cov.: 31 AF XY: 0.374 AC XY: 27761 AN XY: 74248

African (AFR) AF: 0.478 AC: 19790 AN: 41424

American (AMR) AF: 0.378 AC: 5769 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2600 AN: 5146

South Asian (SAS) AF: 0.494 AC: 2377 AN: 4810

European-Finnish (FIN) AF: 0.315 AC: 3334 AN: 10578

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20065 AN: 67904

Other (OTH) AF: 0.351 AC: 738 AN: 2104

Alfa AF: 0.320 Hom.: 6156

Bravo AF: 0.381

TwinsUK AF: 0.299 AC: 1108

ALSPAC AF: 0.303 AC: 1166

ESP6500AA AF: 0.465 AC: 1945

ESP6500EA AF: 0.300 AC: 2531

ExAC AF: 0.370 AC: 44734

Asia WGS AF: 0.470 AC: 1632 AN: 3478

EpiCase AF: 0.294

EpiControl AF: 0.291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.056
BayesDel_addAF	Benign	-0.83	T
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.4
DANN	Benign	0.86
DEOGEN2	Benign	0.053	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.024	N
LIST_S2	Benign	0.022	T
MetaRNN	Benign	0.00029	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	-2.8	N
PhyloP100		1.1
PrimateAI	Benign	0.36	T
PROVEAN	Benign	3.0	N
REVEL	Benign	0.28
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.042
MPC		0.29
ClinPred		0.0047	T
GERP RS		3.1
Varity_R		0.086
gMVP		0.61
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1049793; hg19: chr7-150557665; COSMIC: COSV62867576; COSMIC: COSV62867576;