11-68020059-T-C

Variant names:

• chr11-68020059-T-C
• rs2286169
• NM_000694.4:c.562+263T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000694.4(ALDH3B1):​c.562+263T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,934 control chromosomes in the GnomAD database, including 4,569 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 0.24 (4569 hom., cov: 32)
• Consequence: ALDH3B1 NM_000694.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3B1	NM_000694.4	c.562+263T>C		intron_variant	Intron 6 of 9	ENST00000342456.11	NP_000685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH3B1	ENST00000342456.11	c.562+263T>C		intron_variant	Intron 6 of 9	1	NM_000694.4	ENSP00000473990.2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36446 AN: 151816 Hom.: 4564 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.238

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.240 AC: 36472 AN: 151934 Hom.: 4569 Cov.: 32 AF XY: 0.233 AC XY: 17288 AN XY: 74282

African (AFR) AF: 0.309 AC: 12792 AN: 41380

American (AMR) AF: 0.178 AC: 2726 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1095 AN: 5146

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4816

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

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16158 AN: 67934

Other (OTH) AF: 0.237 AC: 500 AN: 2112

Alfa AF: 0.239 Hom.: 547

Bravo AF: 0.247

Asia WGS AF: 0.215 AC: 746 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	0.93
DANN	Benign	0.35
PhyloP100		-1.0
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: rs2286169; hg19: chr11-67787528;