chr9-94926763-G-A

Variant names:

• chr9-94926763-G-A
• rs4744411
• NM_001193329.3:c.1555-1662G>A

Variant summary

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

The NM_001193329.3(AOPEP):​c.1555-1662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 148,992 control chromosomes in the GnomAD database, including 9,593 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 0.35 (9593 hom., cov: 25)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 12 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]

ENSG00000224764 (HGNC:58217):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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.1555-1662G>A		intron	N/A	NP_001180258.1
	AOPEP	NM_001386066.1		c.1555-1662G>A		intron	N/A	NP_001372995.1
	AOPEP	NM_001386068.1		c.1555-1662G>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.1555-1662G>A		intron	N/A	ENSP00000364464.2
	AOPEP	ENST00000297979.9	TSL:1	c.1365-28414G>A		intron	N/A	ENSP00000297979.5
	AOPEP	ENST00000277198.6	TSL:2	c.1555-1662G>A		intron	N/A	ENSP00000277198.2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 51458 AN: 148868 Hom.: 9590 Cov.: 25

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.345 AC: 51475 AN: 148992 Hom.: 9593 Cov.: 25 AF XY: 0.343 AC XY: 24941 AN XY: 72724

African (AFR) AF: 0.210 AC: 8504 AN: 40508

American (AMR) AF: 0.324 AC: 4865 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1681 AN: 3456

East Asian (EAS) AF: 0.269 AC: 1298 AN: 4822

South Asian (SAS) AF: 0.313 AC: 1417 AN: 4532

European-Finnish (FIN) AF: 0.356 AC: 3647 AN: 10230

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 28891 AN: 67180

Other (OTH) AF: 0.370 AC: 765 AN: 2068

Alfa AF: 0.322 Hom.: 2186

Bravo AF: 0.337

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.51
PhyloP100		-1.4
Mutation Taster		=99/1	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: rs4744411; hg19: chr9-97689045;