dbSNP rs1050884: AOX1:n.3135T>G (chr2-200671058-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000485106.5(AOX1):n.3135T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 181,014 control chromosomes in the GnomAD database, including 489 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 0.062 ( 398 hom., cov: 33)

Exomes 𝑓: 0.066 ( 91 hom. )

Consequence

AOX1
ENST00000485106.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

4 publications found

Variant links:

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]

AOX1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOX1	NM_001159.4 link	c.*379T>G		3_prime_UTR_variant	Exon 35 of 35	ENST00000374700.7	NP_001150.3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
AOX1	ENST00000485106.5 link	n.3135T>G	non_coding_transcript_exon_variant	Exon 22 of 22	1
AOX1	ENST00000374700.7 link	c.*379T>G	3_prime_UTR_variant	Exon 35 of 35	1	NM_001159.4	ENSP00000363832.2
AOX1	ENST00000439380.1 link	c.486+1316T>G	intron_variant	Intron 4 of 4	3		ENSP00000413326.1
AOX1	ENST00000465297.5 link	n.*186T>G	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0622

AC:

9461

AN:

152136

Hom.:

386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0263

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.0529

Gnomad SAS

AF:

0.0896

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0668

Gnomad OTH

AF:

0.0587

GnomAD4 exome

AF:

0.0657

AC:

1890

AN:

28760

Hom.:

Cov.:

AF XY:

0.0666

AC XY:

986

AN XY:

14800

show subpopulations

African (AFR)

AF:

0.0234

AC:

AN:

1112

American (AMR)

AF:

0.112

AC:

247

AN:

2214

Ashkenazi Jewish (ASJ)

AF:

0.0257

AC:

AN:

1168

East Asian (EAS)

AF:

0.0447

AC:

AN:

1902

South Asian (SAS)

AF:

0.0983

AC:

AN:

926

European-Finnish (FIN)

AF:

0.0982

AC:

111

AN:

1130

Middle Eastern (MID)

AF:

0.0154

AC:

AN:

130

European-Non Finnish (NFE)

AF:

0.0640

AC:

1175

AN:

18358

Other (OTH)

AF:

0.0676

AC:

123

AN:

1820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

178

267

356

445

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0625

AC:

9509

AN:

152254

Hom.:

398

Cov.:

AF XY:

0.0649

AC XY:

4830

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0270

AC:

1122

AN:

41548

American (AMR)

AF:

0.111

AC:

1696

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0334

AC:

116

AN:

3470

East Asian (EAS)

AF:

0.0532

AC:

276

AN:

5186

South Asian (SAS)

AF:

0.0901

AC:

435

AN:

4828

European-Finnish (FIN)

AF:

0.110

AC:

1162

AN:

10586

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0669

AC:

4547

AN:

68014

Other (OTH)

AF:

0.0572

AC:

121

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

446

892

1337

1783

2229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0616

Hom.:

958

Bravo

AF:

0.0582

Asia WGS

AF:

0.0690

AC:

240

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.6

(source)

DANN

Benign

0.79

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over