rs13430864

Variant names:

• chr2-200783916-T-G
• rs13430864

Variant summary

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

The variant allele was found at a frequency of 0.0682 in 152,210 control chromosomes in the GnomAD database, including 1,201 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 0.068 (1201 hom., cov: 32)
• Consequence: AOX2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

Genes affected

AOX2P (HGNC:18450): (aldehyde oxidase 2, pseudogene)

BZW1-AS1 (HGNC:40839): (BZW1 antisense RNA 1)

ENSG00000290906 (HGNC:):

AOX3P-AOX2P (HGNC:53766): (AOX3P-AOX2P readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription between two unprocessed unitary pseudogenes, AOX3P (aldehyde oxidase 3, pseudogene) and AOX2P (aldehyde oxidase 2 pseudogene). The individual pseudogene loci are not curated as transcribed regions. Readthrough transcripts contains disrupted open reading frames, relative to functional homologs, and likely do not encode functional proteins. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOX2P		n.200783916T>G		intragenic_variant
BZW1-AS1	NR_110275.1	n.583-3127A>C		intron_variant	Intron 3 of 3
AOX3P-AOX2P	NR_135011.1	n.4203+3102T>G		intron_variant	Intron 30 of 31
AOX3P-AOX2P	NR_135012.1	n.3696+3102T>G		intron_variant	Intron 29 of 30

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BZW1-AS1	ENST00000447972.3	n.583-3127A>C		intron_variant	Intron 3 of 3	5
ENSG00000290906	ENST00000467645.1	n.1294+1478T>G		intron_variant	Intron 12 of 13	5
AOX2P	ENST00000487742.7	n.3191+3102T>G		intron_variant	Intron 24 of 25	6

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10352 AN: 152092 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0682 AC: 10383 AN: 152210 Hom.: 1201 Cov.: 32 AF XY: 0.0663 AC XY: 4931 AN XY: 74420

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0275

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00110

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0119 Hom.: 157

Bravo AF: 0.0758

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13430864; hg19: chr2-201648639;