Genetic Variant ALDH3B1:c.1117-29A>G (chr11-68025980-A-G) – 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.1117-29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,499,684 control chromosomes in the GnomAD database, including 41,766 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 0.26 ( 5658 hom., cov: 31)

Exomes 𝑓: 0.23 ( 36108 hom. )

Consequence

ALDH3B1
NM_000694.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

18 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:

GLTC1 (HGNC:56861):

GLTC1 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3B1	NM_000694.4 link	c.1117-29A>G		intron_variant	Intron 8 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.1117-29A>G		intron_variant	Intron 8 of 9	1	NM_000694.4	ENSP00000473990.2		P43353-1

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39595

AN:

151850

Hom.:

5652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.252

GnomAD2 exomes

AF:

0.211

AC:

34893

AN:

165030

AF XY:

0.214

show subpopulations

Gnomad AFR exome

AF:

0.383

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.211

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.234

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.228

AC:

306918

AN:

1347716

Hom.:

36108

Cov.:

AF XY:

0.228

AC XY:

151420

AN XY:

664458

show subpopulations

African (AFR)

AF:

0.377

AC:

11436

AN:

30320

American (AMR)

AF:

0.129

AC:

4335

AN:

33524

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

4997

AN:

22678

East Asian (EAS)

AF:

0.225

AC:

8005

AN:

35600

South Asian (SAS)

AF:

0.206

AC:

15128

AN:

73334

European-Finnish (FIN)

AF:

0.129

AC:

6470

AN:

50062

Middle Eastern (MID)

AF:

0.223

AC:

1194

AN:

5346

European-Non Finnish (NFE)

AF:

0.233

AC:

242571

AN:

1040980

Other (OTH)

AF:

0.229

AC:

12782

AN:

55872

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

9431

18862

28294

37725

47156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8424

16848

25272

33696

42120

<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:

0.261

AC:

39624

AN:

151968

Hom.:

5658

Cov.:

AF XY:

0.253

AC XY:

18812

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.379

AC:

15713

AN:

41408

American (AMR)

AF:

0.189

AC:

2886

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

703

AN:

3472

East Asian (EAS)

AF:

0.214

AC:

1103

AN:

5162

South Asian (SAS)

AF:

0.211

AC:

1018

AN:

4816

European-Finnish (FIN)

AF:

0.110

AC:

1161

AN:

10594

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.238

AC:

16195

AN:

67952

Other (OTH)

AF:

0.251

AC:

528

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1479

2958

4436

5915

7394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.242

Hom.:

8149

Bravo

AF:

0.270

Asia WGS

AF:

0.217

AC:

753

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.0030

(source)

DANN

Benign

0.63

PhyloP100

-1.8

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