rs391784

Variant names:

• chr9-94813345-T-A
• rs391784
• NM_001193329.3:c.1364+12343T>A

Your query was ambiguous. Multiple possible variants found:

• chr9-94813345-T-A
• chr9-94813345-T-C
• chr9-94813345-T-G

Variant summary

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

The NM_001193329.3(AOPEP):​c.1364+12343T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,014 control chromosomes in the GnomAD database, including 35,946 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 (35946 hom., cov: 31)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOPEP	NM_001193329.3	c.1364+12343T>A		intron_variant	Intron 5 of 16	ENST00000375315.8	NP_001180258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOPEP	ENST00000375315.8	c.1364+12343T>A		intron_variant	Intron 5 of 16	1	NM_001193329.3	ENSP00000364464.2
AOPEP	ENST00000297979.9	c.1364+12343T>A		intron_variant	Intron 5 of 14	1		ENSP00000297979.5
AOPEP	ENST00000277198.6	c.1364+12343T>A		intron_variant	Intron 5 of 7	2		ENSP00000277198.2

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103152 AN: 151896 Hom.: 35902 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.679 AC: 103257 AN: 152014 Hom.: 35946 Cov.: 31 AF XY: 0.682 AC XY: 50655 AN XY: 74288

African (AFR) AF: 0.836 AC: 34673 AN: 41472

American (AMR) AF: 0.693 AC: 10590 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1892 AN: 3470

East Asian (EAS) AF: 0.756 AC: 3898 AN: 5156

South Asian (SAS) AF: 0.746 AC: 3587 AN: 4810

European-Finnish (FIN) AF: 0.648 AC: 6848 AN: 10560

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39611 AN: 67944

Other (OTH) AF: 0.645 AC: 1362 AN: 2110

Alfa AF: 0.624 Hom.: 3779

Bravo AF: 0.689

Asia WGS AF: 0.789 AC: 2744 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	0.93
DANN	Benign	0.28
PhyloP100		-0.43
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: rs391784; hg19: chr9-97575627;