chr7-150855877-A-T

Variant names:

• chr7-150855877-A-T
• rs2268999
• NM_001091.4:c.-16-578A>T

Variant summary

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

The NM_001091.4(AOC1):​c.-16-578A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,434 control chromosomes in the GnomAD database, including 9,704 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 (9704 hom., cov: 32)
• Consequence: AOC1 NM_001091.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOC1	NM_001091.4	c.-16-578A>T		intron_variant	Intron 1 of 4	ENST00000360937.9	NP_001082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000360937.9	c.-16-578A>T		intron_variant	Intron 1 of 4	1	NM_001091.4	ENSP00000354193.4

Frequencies

GnomAD3 genomes AF: 0.330 AC: 49963 AN: 151314 Hom.: 9673 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.330 AC: 50037 AN: 151434 Hom.: 9704 Cov.: 32 AF XY: 0.327 AC XY: 24217 AN XY: 74034

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.284

Alfa AF: 0.302 Hom.: 981

Bravo AF: 0.335

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.098
DANN	Benign	0.44

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: rs2268999; hg19: chr7-150552965;