rs10491560

Variant names:

• chr9-95082231-G-A
• rs10491560
• NM_001193329.3:c.2320-344G>A

Variant summary

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

The NM_001386074.1(AOPEP):​c.*18G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,090 control chromosomes in the GnomAD database, including 3,221 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 0.20 (3221 hom., cov: 32)
• Consequence: AOPEP NM_001386074.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386074.1. 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.2320-344G>A		intron	N/A	NP_001180258.1	Q8N6M6-1
	AOPEP	NM_001386074.1		c.*18G>A		3_prime_UTR	Exon 16 of 16	NP_001373003.1
	AOPEP	NM_001386066.1		c.2319+1451G>A		intron	N/A	NP_001372995.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOPEP	ENST00000375315.8	TSL:1 MANE Select	c.2320-344G>A		intron	N/A	ENSP00000364464.2	Q8N6M6-1
	AOPEP	ENST00000297979.9	TSL:1	c.2023-344G>A		intron	N/A	ENSP00000297979.5	Q8N6M6-2
	AOPEP	ENST00000951986.1		c.2320-344G>A		intron	N/A	ENSP00000622045.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30486 AN: 151972 Hom.: 3223 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.201 AC: 30505 AN: 152090 Hom.: 3221 Cov.: 32 AF XY: 0.200 AC XY: 14904 AN XY: 74358

African (AFR) AF: 0.178 AC: 7393 AN: 41460

American (AMR) AF: 0.180 AC: 2760 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1521 AN: 5186

South Asian (SAS) AF: 0.253 AC: 1217 AN: 4810

European-Finnish (FIN) AF: 0.154 AC: 1625 AN: 10584

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14034 AN: 67972

Other (OTH) AF: 0.208 AC: 439 AN: 2110

Alfa AF: 0.211 Hom.: 13201

Bravo AF: 0.205

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0020
DANN	Benign	0.64
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10491560; hg19: chr9-97844513; COSMIC: COSV52987830; COSMIC: COSV52987830;