rs2286164

Variant names:

• chr11-68025980-A-G
• rs2286164
• NM_000694.4:c.1117-29A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-68025980-A-G
• chr11-68025980-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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 -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.

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.1117-29A>G		intron	N/A	NP_000685.1	P43353-1
	ALDH3B1	NM_001161473.3		c.1117-29A>G		intron	N/A	NP_001154945.1	P43353-1
	ALDH3B1	NM_001030010.3		c.1006-29A>G		intron	N/A	NP_001025181.1	P43353-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH3B1	ENST00000342456.11	TSL:1 MANE Select	c.1117-29A>G		intron	N/A	ENSP00000473990.2	P43353-1
	ALDH3B1	ENST00000614849.4	TSL:1	c.1117-29A>G		intron	N/A	ENSP00000478486.1	P43353-1
	ALDH3B1	ENST00000617288.4	TSL:1	c.1006-29A>G		intron	N/A	ENSP00000481604.1	P43353-2

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

GnomAD2 exomes AF: 0.211 AC: 34893 AN: 165030 AF XY: 0.214

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 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

African (AFR) AF: 0.377 AC: 11436 AN: 30320

American (AMR) AF: 0.129 AC: 4335 AN: 33524

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 4997 AN: 22678

East Asian (EAS) AF: 0.225 AC: 8005 AN: 35600

South Asian (SAS) AF: 0.206 AC: 15128 AN: 73334

European-Finnish (FIN) AF: 0.129 AC: 6470 AN: 50062

Middle Eastern (MID) AF: 0.223 AC: 1194 AN: 5346

European-Non Finnish (NFE) AF: 0.233 AC: 242571 AN: 1040980

Other (OTH) AF: 0.229 AC: 12782 AN: 55872

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

African (AFR) AF: 0.379 AC: 15713 AN: 41408

American (AMR) AF: 0.189 AC: 2886 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 703 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5162

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4816

European-Finnish (FIN) AF: 0.110 AC: 1161 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16195 AN: 67952

Other (OTH) AF: 0.251 AC: 528 AN: 2106

Alfa AF: 0.242 Hom.: 8149

Bravo AF: 0.270

Asia WGS AF: 0.217 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0030
DANN	Benign	0.63
PhyloP100		-1.8
Mutation Taster		=100/0	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: rs2286164; hg19: chr11-67793448; COSMIC: COSV50292337; COSMIC: COSV50292337;