rs4725367

Variant names:

• chr7-150828791-T-C
• rs4725367
• ENST00000726369.1:n.388A>G

Variant summary

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

The ENST00000726369.1(ENSG00000289052):​n.388A>G variant causes a non coding transcript exon 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: ENSG00000289052 ENST00000726369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 7 publications found

Genes affected

ENSG00000289052 (HGNC:):

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]

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375567	XR_928169.3	n.296A>G		non_coding_transcript_exon_variant	Exon 3 of 4
LOC105375567	XR_928171.3	n.296A>G		non_coding_transcript_exon_variant	Exon 3 of 5
LOC124901775	XR_007060591.1	n.257+1358T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289052	ENST00000726369.1	n.388A>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000289052	ENST00000726370.1	n.435A>G		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000289052	ENST00000726371.1	n.435A>G		non_coding_transcript_exon_variant	Exon 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs4725367; hg19: chr7-150525879;