Variant 2-200605631-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001159.4(AOX1):c.907+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0052 in 1,423,636 control chromosomes in the GnomAD database, including 331 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 193 hom., cov: 32)

Exomes 𝑓: 0.0025 ( 138 hom. )

Consequence

AOX1
NM_001159.4 splice_region, intron

Scores

Splicing: ADA: 0.00002854

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.131

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:

AOX1 (HGNC:):

AOX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 2-200605631-G-A is Benign according to our data. Variant chr2-200605631-G-A is described in ClinVar as [Benign]. Clinvar id is 767839.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AOX1	NM_001159.4 linkuse as main transcript	c.907+3G>A		splice_region_variant, intron_variant		ENST00000374700.7	NP_001150.3	Q06278

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AOX1	ENST00000374700.7 linkuse as main transcript	c.907+3G>A		splice_region_variant, intron_variant		1	NM_001159.4	ENSP00000363832.2		Q06278

Frequencies

GnomAD3 genomes

AF:

0.0273

AC:

4143

AN:

151720

Hom.:

191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0957

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00841

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000324

Gnomad OTH

AF:

0.0187

GnomAD3 exomes

AF:

0.00697

AC:

1301

AN:

186618

Hom.:

AF XY:

0.00513

AC XY:

528

AN XY:

102922

show subpopulations

Gnomad AFR exome

AF:

0.0954

Gnomad AMR exome

AF:

0.00380

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000388

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000238

Gnomad OTH exome

AF:

0.00300

GnomAD4 exome

AF:

0.00255

AC:

3239

AN:

1271796

Hom.:

138

Cov.:

AF XY:

0.00234

AC XY:

1481

AN XY:

633500

show subpopulations

Gnomad4 AFR exome

AF:

0.0988

Gnomad4 AMR exome

AF:

0.00475

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000398

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000131

Gnomad4 OTH exome

AF:

0.00495

GnomAD4 genome

AF:

0.0274

AC:

4159

AN:

151840

Hom.:

193

Cov.:

AF XY:

0.0267

AC XY:

1979

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.0958

Gnomad4 AMR

AF:

0.00839

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000324

Gnomad4 OTH

AF:

0.0185

Alfa

AF:

0.0130

Hom.:

Bravo

AF:

0.0308

Asia WGS

AF:

0.00462

AC:

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

6.9

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000029

dbscSNV1_RF

Benign

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over