rs2286164

Positions:

• chr11-68025980-A-G
• chr11-68025980-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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ALDH3B1	NM_000694.4	c.1117-29A>G		intron_variant		ENST00000342456.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH3B1	ENST00000342456.11	c.1117-29A>G		intron_variant		1	NM_000694.4	P1
	ENST00000532296.1	n.341-648T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39595 AN: 151850 Hom.: 5652 Cov.: 31

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

GnomAD3 exomes AF: 0.211 AC: 34893 AN: 165030 Hom.: 4061 AF XY: 0.214 AC XY: 18965 AN XY: 88640

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 SAS exome AF: 0.218

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.: 21 AF XY: 0.228 AC XY: 151420 AN XY: 664458

Gnomad4 AFR exome AF: 0.377

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.220

Gnomad4 EAS exome AF: 0.225

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.129

Gnomad4 NFE exome AF: 0.233

Gnomad4 OTH exome AF: 0.229

GnomAD4 genome AF: 0.261 AC: 39624 AN: 151968 Hom.: 5658 Cov.: 31 AF XY: 0.253 AC XY: 18812 AN XY: 74294

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.251

Alfa AF: 0.239 Hom.: 6232

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
DANN	Benign	0.63

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: rs2286164; hg19: chr11-67793448; COSMIC: COSV50292337; COSMIC: COSV50292337;