rs2071517

chr7-150861311-G-Achr7-150861311-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

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]

LOC105375567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOC1	NM_001091.4	c.*102G>A		3_prime_UTR_variant	5/5	ENST00000360937.9
LOC105375567	XR_928171.3	n.122+15698C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOC1	ENST00000360937.9	c.*102G>A		3_prime_UTR_variant	5/5	1	NM_001091.4	P2
AOC1	ENST00000467291.5	c.*102G>A		3_prime_UTR_variant	7/7	5		P2
AOC1	ENST00000493429.5	c.*102G>A		3_prime_UTR_variant	7/7	5		P2
AOC1	ENST00000416793.6			downstream_gene_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34748 AN: 151910 Hom.: 4408 Cov.: 32

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.: 20 AF XY: 0.210 AC XY: 123995 AN XY: 589398

Gnomad4 AFR exome AF: 0.238

Gnomad4 AMR exome AF: 0.325

Gnomad4 ASJ exome AF: 0.294

Gnomad4 EAS exome AF: 0.521

Gnomad4 SAS exome AF: 0.353

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.227

GnomAD4 genome AF: 0.229 AC: 34770 AN: 152030 Hom.: 4413 Cov.: 32 AF XY: 0.234 AC XY: 17357 AN XY: 74300

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.223

Alfa AF: 0.198 Hom.: 4316

Bravo AF: 0.237

Asia WGS AF: 0.378 AC: 1308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.58

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

LitVar

Other links and lift over

dbSNP: rs2071517; hg19: chr7-150558399;