dbSNP rs308338: ALDH3B1:c.-2+80G>A (chr11-68008772-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001161473.3(ALDH3B1):c.-2+80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,220 control chromosomes in the GnomAD database, including 19,059 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 0.49 ( 19050 hom., cov: 34)

Exomes 𝑓: 0.41 ( 9 hom. )

Consequence

ALDH3B1
NM_001161473.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

8 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:

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001161473.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH3B1	NM_001161473.3		c.-2+80G>A		intron	N/A	NP_001154945.1	P43353-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH3B1	ENST00000614849.4	TSL:1	c.-2+80G>A		intron	N/A	ENSP00000478486.1	P43353-1
	ALDH3B1	ENST00000894326.1		c.-2+80G>A		intron	N/A	ENSP00000564385.1

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74752

AN:

152004

Hom.:

19022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.660

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.427

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.466

GnomAD4 exome

AF:

0.408

AC:

AN:

Hom.:

AF XY:

0.394

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.353

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.548

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.492

AC:

74831

AN:

152122

Hom.:

19050

Cov.:

AF XY:

0.486

AC XY:

36126

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.622

AC:

25797

AN:

41488

American (AMR)

AF:

0.393

AC:

6018

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.388

AC:

1347

AN:

3472

East Asian (EAS)

AF:

0.374

AC:

1930

AN:

5162

South Asian (SAS)

AF:

0.395

AC:

1902

AN:

4820

European-Finnish (FIN)

AF:

0.427

AC:

4528

AN:

10604

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.465

AC:

31627

AN:

67950

Other (OTH)

AF:

0.462

AC:

976

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1925

3850

5775

7700

9625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

662

1324

1986

2648

3310

<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:

0.459

Hom.:

24031

Bravo

AF:

0.494

Asia WGS

AF:

0.397

AC:

1381

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.84

PhyloP100

-1.2

PromoterAI

-0.070

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over