dbSNP rs581105: ALDH3B1:c.163-442A>C (chr11-68018085-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000694.4(ALDH3B1):c.163-442A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 156,284 control chromosomes in the GnomAD database, including 18,475 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 0.48 ( 18036 hom., cov: 33)

Exomes 𝑓: 0.43 ( 439 hom. )

Consequence

ALDH3B1
NM_000694.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473

Publications

4 publications found

Variant links:

Genes affected

ALDH3B1 (HGNC:410): (aldehyde dehydrogenase 3 family member B1) This gene encodes a member of the aldehyde dehydrogenase protein family. Aldehyde dehydrogenases are a family of isozymes that may play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. The encoded protein is able to oxidize long-chain fatty aldehydes in vitro, and may play a role in protection from oxidative stress. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ALDH3B1 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3B1	NM_000694.4 link	c.163-442A>C		intron_variant	Intron 2 of 9	ENST00000342456.11	NP_000685.1	P43353-1A0A024R5D8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH3B1	ENST00000342456.11 link	c.163-442A>C		intron_variant	Intron 2 of 9	1	NM_000694.4	ENSP00000473990.2		P43353-1

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73006

AN:

151928

Hom.:

18017

Cov.:

show subpopulations

Gnomad AFR

AF:

0.583

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.422

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.447

GnomAD4 exome

AF:

0.426

AC:

1805

AN:

4238

Hom.:

439

Cov.:

AF XY:

0.425

AC XY:

989

AN XY:

2326

show subpopulations

African (AFR)

AF:

0.583

AC:

AN:

American (AMR)

AF:

0.246

AC:

AN:

248

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

AN:

East Asian (EAS)

AF:

0.303

AC:

AN:

South Asian (SAS)

AF:

0.374

AC:

175

AN:

468

European-Finnish (FIN)

AF:

0.439

AC:

AN:

148

Middle Eastern (MID)

AF:

0.143

AC:

AN:

European-Non Finnish (NFE)

AF:

0.453

AC:

1320

AN:

2914

Other (OTH)

AF:

0.430

AC:

104

AN:

242

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

148

198

247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.481

AC:

73072

AN:

152046

Hom.:

18036

Cov.:

AF XY:

0.474

AC XY:

35252

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.583

AC:

24184

AN:

41482

American (AMR)

AF:

0.387

AC:

5925

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.392

AC:

1361

AN:

3470

East Asian (EAS)

AF:

0.372

AC:

1908

AN:

5132

South Asian (SAS)

AF:

0.395

AC:

1904

AN:

4824

European-Finnish (FIN)

AF:

0.422

AC:

4462

AN:

10568

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.466

AC:

31698

AN:

67960

Other (OTH)

AF:

0.445

AC:

938

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1972

3944

5916

7888

9860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.462

Hom.:

2705

Bravo

AF:

0.481

Asia WGS

AF:

0.390

AC:

1356

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

(source)

DANN

Benign

0.66

PhyloP100

-0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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