7-150847046-C-T

Variant names:

• chr7-150847046-C-T
• rs10240738
• ENST00000467291.5:c.-92-5069C>T

Variant summary

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

The ENST00000467291.5(AOC1):​c.-92-5069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,036 control chromosomes in the GnomAD database, including 28,540 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 0.59 (28540 hom., cov: 32)
• Consequence: AOC1 ENST00000467291.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

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]

LOC105375567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375567	XR_928169.3	n.123-5601G>A		intron_variant	Intron 1 of 3
LOC105375567	XR_928171.3	n.123-5601G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000467291.5	c.-92-5069C>T		intron_variant	Intron 2 of 6	5		ENSP00000418328.1
AOC1	ENST00000493429.5	c.-92-5069C>T		intron_variant	Intron 2 of 6	5		ENSP00000418614.1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89485 AN: 151920 Hom.: 28486 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.589 AC: 89596 AN: 152036 Hom.: 28540 Cov.: 32 AF XY: 0.591 AC XY: 43941 AN XY: 74292

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.536

Alfa AF: 0.537 Hom.: 5201

Bravo AF: 0.615

Asia WGS AF: 0.651 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.43

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: rs10240738; hg19: chr7-150544134;