rs4725367

Variant names:

• chr7-150828791-T-C
• rs4725367
• ENST00000941409.1:c.-93+2340T>C

Variant summary

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

The ENST00000941409.1(AOC1):​c.-93+2340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,104 control chromosomes in the GnomAD database, including 10,415 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 0.36 (10415 hom., cov: 32)
• Consequence: AOC1 ENST00000941409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 7 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 (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC1	ENST00000941409.1		c.-93+2340T>C		intron	N/A	ENSP00000611468.1
	AOC1	ENST00000467291.5	TSL:5	c.-93+1389T>C		intron	N/A	ENSP00000418328.1	P19801-1
	AOC1	ENST00000493429.5	TSL:5	c.-93+1389T>C		intron	N/A	ENSP00000418614.1	P19801-1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54292 AN: 151986 Hom.: 10413 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.394

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.357 AC: 54316 AN: 152104 Hom.: 10415 Cov.: 32 AF XY: 0.350 AC XY: 26037 AN XY: 74344

African (AFR) AF: 0.254 AC: 10520 AN: 41492

American (AMR) AF: 0.339 AC: 5175 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1170 AN: 3472

East Asian (EAS) AF: 0.102 AC: 527 AN: 5190

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4812

European-Finnish (FIN) AF: 0.343 AC: 3630 AN: 10572

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30543 AN: 67966

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.415 Hom.: 7699

Bravo AF: 0.349

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		0.082
Mutation Taster		=100/0	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4725367;

hg19: chr7-150525879;