11-68026041-C-T

Variant names:

• chr11-68026041-C-T
• rs2286163
• NM_000694.4:c.1149C>T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_000694.4(ALDH3B1):​c.1149C>T​(p.Ser383Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,607,152 control chromosomes in the GnomAD database, including 42,243 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 0.23 (4019 hom., cov: 32)
  • Exomes 𝑓: 0.23 (38224 hom.)
• Consequence: ALDH3B1 NM_000694.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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]

ENSG00000255306 (HGNC:56861):

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BP7: Synonymous conserved (PhyloP=-1.58 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3B1	NM_000694.4	c.1149C>T	p.Ser383Ser	synonymous_variant	Exon 9 of 10	ENST00000342456.11	NP_000685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH3B1	ENST00000342456.11	c.1149C>T	p.Ser383Ser	synonymous_variant	Exon 9 of 10	1	NM_000694.4	ENSP00000473990.2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34349 AN: 152010 Hom.: 4018 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.227

GnomAD3 exomes AF: 0.203 AC: 48863 AN: 240696 Hom.: 5292 AF XY: 0.206 AC XY: 26987 AN XY: 130822

Gnomad AFR exome AF: 0.263

Gnomad AMR exome AF: 0.112

Gnomad ASJ exome AF: 0.215

Gnomad EAS exome AF: 0.212

Gnomad SAS exome AF: 0.211

Gnomad FIN exome AF: 0.120

Gnomad NFE exome AF: 0.233

Gnomad OTH exome AF: 0.211

GnomAD4 exome AF: 0.226 AC: 329518 AN: 1455024 Hom.: 38224 Cov.: 32 AF XY: 0.226 AC XY: 163832 AN XY: 723422

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.219

Gnomad4 EAS exome AF: 0.225

Gnomad4 SAS exome AF: 0.207

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.236

Gnomad4 OTH exome AF: 0.223

GnomAD4 genome AF: 0.226 AC: 34367 AN: 152128 Hom.: 4019 Cov.: 32 AF XY: 0.219 AC XY: 16309 AN XY: 74374

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.226

Alfa AF: 0.230 Hom.: 6647

Bravo AF: 0.230

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	9.6
DANN	Benign	0.77

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: rs2286163; hg19: chr11-67793509; COSMIC: COSV50288499; COSMIC: COSV50288499;