chr9-94822736-G-T

Position:

• chr9-94822736-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001193329.3(AOPEP):​c.1364+21734G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,102 control chromosomes in the GnomAD database, including 47,280 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 0.77 (47280 hom., cov: 33)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOPEP	NM_001193329.3	c.1364+21734G>T		intron_variant		ENST00000375315.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOPEP	ENST00000375315.8	c.1364+21734G>T		intron_variant		1	NM_001193329.3	P1
AOPEP	ENST00000297979.9	c.1364+21734G>T		intron_variant		1
AOPEP	ENST00000277198.6	c.1364+21734G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117666 AN: 151984 Hom.: 47285 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.774 AC: 117691 AN: 152102 Hom.: 47280 Cov.: 33 AF XY: 0.774 AC XY: 57542 AN XY: 74376

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.811

Alfa AF: 0.769 Hom.: 1980

Bravo AF: 0.761

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.019
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs732141; hg19: chr9-97585018;