9-94872076-A-T

Position:

• chr9-94872076-A-T

Variant summary

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

The NM_001193329.3(AOPEP):​c.1365-51910A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,166 control chromosomes in the GnomAD database, including 57,369 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 0.86 (57369 hom., cov: 31)
• Consequence: AOPEP NM_001193329.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

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]

AOPEP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AOPEP	NM_001193329.3	c.1365-51910A>T		intron_variant		ENST00000375315.8	NP_001180258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AOPEP	ENST00000375315.8	c.1365-51910A>T		intron_variant		1	NM_001193329.3	ENSP00000364464.2
AOPEP	ENST00000297979.9	c.1364+71074A>T		intron_variant		1		ENSP00000297979.5
AOPEP	ENST00000277198.6	c.1365-51910A>T		intron_variant		2		ENSP00000277198.2

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130407 AN: 152048 Hom.: 57367 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.857 AC: 130451 AN: 152166 Hom.: 57369 Cov.: 31 AF XY: 0.860 AC XY: 63976 AN XY: 74388

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.886

Alfa AF: 0.890 Hom.: 6757

Bravo AF: 0.843

Asia WGS AF: 0.889 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.1
DANN	Benign	0.63

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: rs2406898; hg19: chr9-97634358;