rs308337

chr11-68008822-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000614849.4(ALDH3B1):c.-2+130C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,518 control chromosomes in the GnomAD database, including 551 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 0.050 (551 hom., cov: 33)
  • Exomes 𝑓: 0.0082 (0 hom.)
• Consequence: ALDH3B1 ENST00000614849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH3B1	NM_001161473.3	c.-2+130C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH3B1	ENST00000614849.4	c.-2+130C>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7578 AN: 152156 Hom.: 548 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00432

Gnomad OTH AF: 0.0311

GnomAD4 exome AF: 0.00820 AC: 2 AN: 244 Hom.: 0 AF XY: 0.0101 AC XY: 2 AN XY: 198

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.0499 AC: 7593 AN: 152274 Hom.: 551 Cov.: 33 AF XY: 0.0492 AC XY: 3662 AN XY: 74454

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0194

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.0733

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.00432

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0303 Hom.: 50

Bravo AF: 0.0555

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.21
Dann	Benign	0.76

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

Other links and lift over

dbSNP: rs308337; hg19: chr11-67776292;