Variant rs1800869 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000382.3(ALDH3A2):c.940+53C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,602,854 control chromosomes in the GnomAD database, including 50,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3577 hom., cov: 32)

Exomes 𝑓: 0.25 ( 47277 hom. )

Consequence

ALDH3A2
NM_000382.3 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.275

Variant links:

Genes affected

ALDH3A2 (HGNC:403): (aldehyde dehydrogenase 3 family member A2) Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ALDH3A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018155575).

BP6

Variant 17-19661321-C-G is Benign according to our data. Variant chr17-19661321-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1184631.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-19661321-C-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH3A2	NM_000382.3 linkuse as main transcript	c.940+53C>G		intron_variant		ENST00000176643.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH3A2	ENST00000176643.11 linkuse as main transcript	c.940+53C>G		intron_variant		1	NM_000382.3	P1	P51648-1

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30327

AN:

151952

Hom.:

3572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0707

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.272

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.0892

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.190

GnomAD3 exomes

AF:

0.240

AC:

60156

AN:

250216

Hom.:

7937

AF XY:

0.238

AC XY:

32266

AN XY:

135508

show subpopulations

Gnomad AFR exome

AF:

0.0640

Gnomad AMR exome

AF:

0.305

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.394

Gnomad SAS exome

AF:

0.222

Gnomad FIN exome

AF:

0.211

Gnomad NFE exome

AF:

0.240

Gnomad OTH exome

AF:

0.223

GnomAD4 exome

AF:

0.249

AC:

361771

AN:

1450784

Hom.:

47277

Cov.:

AF XY:

0.248

AC XY:

178917

AN XY:

722498

show subpopulations

Gnomad4 AFR exome

AF:

0.0618

Gnomad4 AMR exome

AF:

0.301

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.437

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.215

Gnomad4 NFE exome

AF:

0.254

Gnomad4 OTH exome

AF:

0.232

GnomAD4 genome

AF:

0.200

AC:

30347

AN:

152070

Hom.:

3577

Cov.:

AF XY:

0.201

AC XY:

14971

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.0705

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.387

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.193

Alfa

AF:

0.214

Hom.:

793

Bravo

AF:

0.197

TwinsUK

AF:

0.250

AC:

928

ALSPAC

AF:

0.248

AC:

957

ExAC

AF:

0.235

AC:

28562

Asia WGS

AF:

0.274

AC:

951

AN:

3478

EpiCase

AF:

0.229

EpiControl

AF:

0.225

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Sjögren-Larsson syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 10, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

1.5

DANN

Benign

0.68

FATHMM_MKL

Benign

0.074

LIST_S2

Benign

0.20

MetaRNN

Benign

0.0018

MutationTaster

Benign

1.0

P;P;P;P;P

GERP RS

2.2

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

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