chr7-150832361-T-C

Variant names:

• chr7-150832361-T-C
• rs17173637
• ENST00000467291.5:c.-93+4959T>C

Variant summary

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

The ENST00000467291.5(AOC1):​c.-93+4959T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0801 in 152,296 control chromosomes in the GnomAD database, including 565 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 0.080 (565 hom., cov: 32)
• Consequence: AOC1 ENST00000467291.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 48 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0897 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.-93+4959T>C		intron	N/A	ENSP00000418328.1
	AOC1	ENST00000493429.5	TSL:5	c.-93+4959T>C		intron	N/A	ENSP00000418614.1
	ENSG00000289052	ENST00000726369.1		n.271-3453A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12190 AN: 152178 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0801 AC: 12199 AN: 152296 Hom.: 565 Cov.: 32 AF XY: 0.0815 AC XY: 6066 AN XY: 74474

African (AFR) AF: 0.0628 AC: 2610 AN: 41574

American (AMR) AF: 0.0538 AC: 824 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0949 AC: 329 AN: 3468

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5184

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1628 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6230 AN: 68014

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0856 Hom.: 1899

Bravo AF: 0.0705

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-1.3
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: rs17173637; hg19: chr7-150529449;