chr9-94920506-A-G

Position:

• chr9-94920506-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOPEP	NM_001193329.3	c.1365-3480A>G		intron_variant		ENST00000375315.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOPEP	ENST00000375315.8	c.1365-3480A>G		intron_variant		1	NM_001193329.3	P1
AOPEP	ENST00000297979.9	c.1365-34671A>G		intron_variant		1
AOPEP	ENST00000277198.6	c.1365-3480A>G		intron_variant		2
AOPEP	ENST00000488186.5	n.121+171A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.0751

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0671 Hom.: 252

Bravo AF: 0.121

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.29

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

Publications

LitVar

Other links and lift over

dbSNP: rs7029570; hg19: chr9-97682788;