rs6977381

Variant names:

• chr7-150845558-G-A
• rs6977381
• ENST00000941409.1:c.-92-6557G>A

Variant summary

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

The ENST00000941409.1(AOC1):​c.-92-6557G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,078 control chromosomes in the GnomAD database, including 33,838 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 0.65 (33838 hom., cov: 32)
• Consequence: AOC1 ENST00000941409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 9 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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.-92-6557G>A		intron	N/A	ENSP00000611468.1
	AOC1	ENST00000467291.5	TSL:5	c.-92-6557G>A		intron	N/A	ENSP00000418328.1	P19801-1
	AOC1	ENST00000493429.5	TSL:5	c.-92-6557G>A		intron	N/A	ENSP00000418614.1	P19801-1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99498 AN: 151960 Hom.: 33789 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.655 AC: 99605 AN: 152078 Hom.: 33838 Cov.: 32 AF XY: 0.658 AC XY: 48932 AN XY: 74328

African (AFR) AF: 0.835 AC: 34660 AN: 41492

American (AMR) AF: 0.662 AC: 10107 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3990 AN: 5162

South Asian (SAS) AF: 0.663 AC: 3199 AN: 4822

European-Finnish (FIN) AF: 0.600 AC: 6337 AN: 10570

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37113 AN: 67968

Other (OTH) AF: 0.603 AC: 1275 AN: 2114

Alfa AF: 0.581 Hom.: 113846

Bravo AF: 0.668

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.25
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: rs6977381;

hg19: chr7-150542646;