NM_001193329.3:c.1365-3480A>G

Variant names:

• chr9-94920506-A-G
• rs7029570
• NM_001193329.3:c.1365-3480A>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.1365-3480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,170 control chromosomes in the GnomAD database, including 1,819 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 0.11 (1819 hom., cov: 32)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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.1365-3480A>G		intron	N/A	NP_001180258.1	Q8N6M6-1
	AOPEP	NM_001386066.1		c.1365-3480A>G		intron	N/A	NP_001372995.1
	AOPEP	NM_001386068.1		c.1365-3480A>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.1365-3480A>G		intron	N/A	ENSP00000364464.2	Q8N6M6-1
	AOPEP	ENST00000297979.9	TSL:1	c.1365-34671A>G		intron	N/A	ENSP00000297979.5	Q8N6M6-2
	AOPEP	ENST00000951986.1		c.1365-3480A>G		intron	N/A	ENSP00000622045.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16570 AN: 152052 Hom.: 1806 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.109 AC: 16623 AN: 152170 Hom.: 1819 Cov.: 32 AF XY: 0.108 AC XY: 8014 AN XY: 74414

African (AFR) AF: 0.279 AC: 11595 AN: 41496

American (AMR) AF: 0.0963 AC: 1472 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3470

East Asian (EAS) AF: 0.0751 AC: 387 AN: 5152

South Asian (SAS) AF: 0.0917 AC: 442 AN: 4818

European-Finnish (FIN) AF: 0.0174 AC: 185 AN: 10624

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0331 AC: 2254 AN: 68002

Other (OTH) AF: 0.0909 AC: 192 AN: 2112

Alfa AF: 0.0730 Hom.: 346

Bravo AF: 0.121

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.29
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7029570; hg19: chr9-97682788;