chr11-68026041-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

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]

GLTC1 (HGNC:56861):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000694.4. 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_000694.4	MANE Select	c.1149C>T	p.Ser383Ser	synonymous	Exon 9 of 10	NP_000685.1
	ALDH3B1	NM_001161473.3		c.1149C>T	p.Ser383Ser	synonymous	Exon 9 of 10	NP_001154945.1
	ALDH3B1	NM_001030010.3		c.1038C>T	p.Ser346Ser	synonymous	Exon 8 of 9	NP_001025181.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH3B1	ENST00000342456.11	TSL:1 MANE Select	c.1149C>T	p.Ser383Ser	synonymous	Exon 9 of 10	ENSP00000473990.2
	ALDH3B1	ENST00000614849.4	TSL:1	c.1149C>T	p.Ser383Ser	synonymous	Exon 9 of 10	ENSP00000478486.1
	ALDH3B1	ENST00000617288.4	TSL:1	c.1038C>T	p.Ser346Ser	synonymous	Exon 8 of 9	ENSP00000481604.1

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

GnomAD2 exomes AF: 0.203 AC: 48863 AN: 240696 AF XY: 0.206

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 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

African (AFR) AF: 0.259 AC: 8630 AN: 33310

American (AMR) AF: 0.120 AC: 5279 AN: 43938

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 5708 AN: 26006

East Asian (EAS) AF: 0.225 AC: 8850 AN: 39276

South Asian (SAS) AF: 0.207 AC: 17570 AN: 84886

European-Finnish (FIN) AF: 0.130 AC: 6932 AN: 53214

Middle Eastern (MID) AF: 0.213 AC: 1223 AN: 5742

European-Non Finnish (NFE) AF: 0.236 AC: 261924 AN: 1108562

Other (OTH) AF: 0.223 AC: 13402 AN: 60090

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

African (AFR) AF: 0.261 AC: 10847 AN: 41488

American (AMR) AF: 0.172 AC: 2630 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5170

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1163 AN: 10592

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16110 AN: 67984

Other (OTH) AF: 0.226 AC: 478 AN: 2112

Alfa AF: 0.232 Hom.: 16703

Bravo AF: 0.230

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	9.6
DANN	Benign	0.77
PhyloP100		-1.6
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

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