chr7-150842063-A-G

Variant names:

• chr7-150842063-A-G
• rs6956432
• ENST00000467291.5:c.-92-10052A>G

Variant summary

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

The ENST00000467291.5(AOC1):​c.-92-10052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,054 control chromosomes in the GnomAD database, including 8,647 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 0.33 (8647 hom., cov: 31)
• Consequence: AOC1 ENST00000467291.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467291.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOC1	ENST00000467291.5	TSL:5	c.-92-10052A>G		intron	N/A	ENSP00000418328.1
	AOC1	ENST00000493429.5	TSL:5	c.-92-10052A>G		intron	N/A	ENSP00000418614.1
	ENSG00000289052	ENST00000726369.1		n.271-13155T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50569 AN: 151936 Hom.: 8638 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.333 AC: 50605 AN: 152054 Hom.: 8647 Cov.: 31 AF XY: 0.336 AC XY: 24961 AN XY: 74316

African (AFR) AF: 0.378 AC: 15687 AN: 41476

American (AMR) AF: 0.328 AC: 5010 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1155 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1206 AN: 4810

European-Finnish (FIN) AF: 0.401 AC: 4227 AN: 10542

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21369 AN: 67984

Other (OTH) AF: 0.300 AC: 633 AN: 2112

Alfa AF: 0.314 Hom.: 4197

Bravo AF: 0.329

Asia WGS AF: 0.288 AC: 1005 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	0.47
DANN	Benign	0.32
PhyloP100		-3.4
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

Other links and lift over

dbSNP: rs6956432; hg19: chr7-150539151;