rs2715898

Variant names:

• chr2-200691665-C-T
• rs2715898
• ENST00000491025.6:n.701-207C>T

Variant summary

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

The ENST00000491025.6(AOX3P):​n.701-207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,860 control chromosomes in the GnomAD database, including 14,344 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 0.43 (14344 hom., cov: 30)
• Consequence: AOX3P ENST00000491025.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 1 publications found

Genes affected

AOX3P (HGNC:19049): (aldehyde oxidase 3, pseudogene) Predicted to enable aldehyde oxidase activity; electron transfer activity; and molybdenum ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOX3P	ENST00000491025.6	n.701-207C>T		intron_variant	Intron 4 of 18	6

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65345 AN: 151742 Hom.: 14334 Cov.: 30

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.431 AC: 65385 AN: 151860 Hom.: 14344 Cov.: 30 AF XY: 0.427 AC XY: 31674 AN XY: 74236

African (AFR) AF: 0.398 AC: 16488 AN: 41386

American (AMR) AF: 0.373 AC: 5701 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2007 AN: 5146

South Asian (SAS) AF: 0.498 AC: 2397 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3108 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32270 AN: 67892

Other (OTH) AF: 0.435 AC: 918 AN: 2112

Alfa AF: 0.471 Hom.: 17725

Bravo AF: 0.432

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.66
PhyloP100		0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2715898; hg19: chr2-201556388;