rs581105

chr11-68018085-A-Cchr11-68018085-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

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=-0.91).
• 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/exons	MANE	UniProt
ALDH3B1	NM_000694.4	c.163-442A>C		intron_variant		ENST00000342456.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH3B1	ENST00000342456.11	c.163-442A>C		intron_variant		1	NM_000694.4	P1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73006 AN: 151928 Hom.: 18017 Cov.: 33

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.: 0 AF XY: 0.425 AC XY: 989 AN XY: 2326

Gnomad4 AFR exome AF: 0.583

Gnomad4 AMR exome AF: 0.246

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.303

Gnomad4 SAS exome AF: 0.374

Gnomad4 FIN exome AF: 0.439

Gnomad4 NFE exome AF: 0.453

Gnomad4 OTH exome AF: 0.430

GnomAD4 genome AF: 0.481 AC: 73072 AN: 152046 Hom.: 18036 Cov.: 33 AF XY: 0.474 AC XY: 35252 AN XY: 74324

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.445

Alfa AF: 0.458 Hom.: 2569

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
Dann	Benign	0.66

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

LitVar

Other links and lift over

dbSNP: rs581105; hg19: chr11-67785555; COSMIC: COSV50288201; COSMIC: COSV50288201;