rs1867102

Variant names:

• chr9-94865485-A-G
• rs1867102
• NM_001193329.3:c.1365-58501A>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.1365-58501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,084 control chromosomes in the GnomAD database, including 14,229 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 0.43 (14229 hom., cov: 32)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOPEP	NM_001193329.3	MANE Select	c.1365-58501A>G		intron	N/A	NP_001180258.1	Q8N6M6-1
	AOPEP	NM_001386066.1		c.1365-58501A>G		intron	N/A	NP_001372995.1
	AOPEP	NM_001386068.1		c.1365-58501A>G		intron	N/A	NP_001372997.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOPEP	ENST00000375315.8	TSL:1 MANE Select	c.1365-58501A>G		intron	N/A	ENSP00000364464.2	Q8N6M6-1
	AOPEP	ENST00000297979.9	TSL:1	c.1364+64483A>G		intron	N/A	ENSP00000297979.5	Q8N6M6-2
	AOPEP	ENST00000951986.1		c.1365-58501A>G		intron	N/A	ENSP00000622045.1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64738 AN: 151966 Hom.: 14231 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.426 AC: 64741 AN: 152084 Hom.: 14229 Cov.: 32 AF XY: 0.428 AC XY: 31817 AN XY: 74344

African (AFR) AF: 0.306 AC: 12703 AN: 41490

American (AMR) AF: 0.461 AC: 7052 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3464

East Asian (EAS) AF: 0.581 AC: 2999 AN: 5164

South Asian (SAS) AF: 0.486 AC: 2344 AN: 4824

European-Finnish (FIN) AF: 0.482 AC: 5090 AN: 10562

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31543 AN: 67976

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.456 Hom.: 8405

Bravo AF: 0.421

Asia WGS AF: 0.516 AC: 1794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.70
PhyloP100		0.96
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: rs1867102; hg19: chr9-97627767;