rs2241080

Variant names:

• chr2-200662516-G-A
• rs2241080
• NM_001159.4:c.3429-339G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-200662516-G-A
• chr2-200662516-G-T

Variant summary

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

The NM_001159.4(AOX1):​c.3429-339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,858 control chromosomes in the GnomAD database, including 6,448 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 0.28 (6448 hom., cov: 32)
• Consequence: AOX1 NM_001159.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

AOX1 (HGNC:553): (aldehyde oxidase 1) Aldehyde oxidase produces hydrogen peroxide and, under certain conditions, can catalyze the formation of superoxide. Aldehyde oxidase is a candidate gene for amyotrophic lateral sclerosis. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOX1	NM_001159.4	c.3429-339G>A		intron_variant	Intron 30 of 34	ENST00000374700.7	NP_001150.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOX1	ENST00000374700.7	c.3429-339G>A		intron_variant	Intron 30 of 34	1	NM_001159.4	ENSP00000363832.2
AOX1	ENST00000485106.5	n.2168-339G>A		intron_variant	Intron 17 of 21	1
AOX1	ENST00000260930.10	c.87-339G>A		intron_variant	Intron 2 of 6	5		ENSP00000260930.6
AOX1	ENST00000465297.5	n.2361-339G>A		intron_variant	Intron 18 of 22	2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42520 AN: 151740 Hom.: 6437 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.280 AC: 42572 AN: 151858 Hom.: 6448 Cov.: 32 AF XY: 0.289 AC XY: 21413 AN XY: 74204

African (AFR) AF: 0.293 AC: 12123 AN: 41400

American (AMR) AF: 0.355 AC: 5426 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3462

East Asian (EAS) AF: 0.538 AC: 2765 AN: 5142

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4804

European-Finnish (FIN) AF: 0.372 AC: 3915 AN: 10520

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15317 AN: 67948

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.239 Hom.: 19604

Bravo AF: 0.283

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.46
PhyloP100		0.011
PromoterAI		0.0040	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs2241080; hg19: chr2-201527239;