rs4725367

chr7-150828791-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928171.3(LOC105375567):n.296A>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: LOC105375567 XR_928171.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

LOC105375567 (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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375567	XR_928171.3	n.296A>G		non_coding_transcript_exon_variant	3/5
LOC124901775	XR_007060591.1	n.257+1358T>C		intron_variant, non_coding_transcript_variant
LOC105375567	XR_928169.3	n.296A>G		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOC1	ENST00000467291.5	c.-93+1389T>C		intron_variant		5		P2
AOC1	ENST00000493429.5	c.-93+1389T>C		intron_variant		5		P2

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

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.393

Alfa AF: 0.414 Hom.: 6962

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4725367; hg19: chr7-150525879;