rs2584806

Variant names:

• chr9-94766996-C-A
• rs2584806
• NM_001193329.3:c.798-6006C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-94766996-C-A
• chr9-94766996-C-G
• chr9-94766996-C-T

Variant summary

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

The NM_001193329.3(AOPEP):​c.798-6006C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,828 control chromosomes in the GnomAD database, including 35,816 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 0.68 (35816 hom., cov: 30)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 8 publications found

Genes affected

AOPEP (HGNC:1361): (aminopeptidase O (putative)) This gene encodes a member of the M1 zinc aminopeptidase family. The encoded protein is a zinc-dependent metallopeptidase that catalyzes the removal of an amino acid from the amino terminus of a protein or peptide. This protein may play a role in the generation of angiotensin IV. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001193329.3. 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
	AOPEP	NM_001193329.3	MANE Select	c.798-6006C>A		intron	N/A	NP_001180258.1
	AOPEP	NM_001386066.1		c.798-6006C>A		intron	N/A	NP_001372995.1
	AOPEP	NM_001386068.1		c.798-6006C>A		intron	N/A	NP_001372997.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOPEP	ENST00000375315.8	TSL:1 MANE Select	c.798-6006C>A		intron	N/A	ENSP00000364464.2
	AOPEP	ENST00000297979.9	TSL:1	c.798-6006C>A		intron	N/A	ENSP00000297979.5
	AOPEP	ENST00000277198.6	TSL:2	c.798-6006C>A		intron	N/A	ENSP00000277198.2

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102887 AN: 151710 Hom.: 35772 Cov.: 30

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.678 AC: 102992 AN: 151828 Hom.: 35816 Cov.: 30 AF XY: 0.681 AC XY: 50557 AN XY: 74202

African (AFR) AF: 0.835 AC: 34605 AN: 41448

American (AMR) AF: 0.693 AC: 10561 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1816 AN: 3466

East Asian (EAS) AF: 0.764 AC: 3934 AN: 5152

South Asian (SAS) AF: 0.747 AC: 3595 AN: 4812

European-Finnish (FIN) AF: 0.649 AC: 6814 AN: 10492

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39506 AN: 67902

Other (OTH) AF: 0.647 AC: 1363 AN: 2106

Alfa AF: 0.618 Hom.: 4231

Bravo AF: 0.688

Asia WGS AF: 0.791 AC: 2749 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.11
PhyloP100		-0.64
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: rs2584806; hg19: chr9-97529278;