12-111809150-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000690.4(ALDH2):c.1522-393C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,070 control chromosomes in the GnomAD database, including 13,895 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 0.35 (13895 hom., cov: 32)
• Consequence: ALDH2 NM_000690.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

Genes affected

ALDH2 (HGNC:404): (aldehyde dehydrogenase 2 family member) This protein belongs to the aldehyde dehydrogenase family of proteins. Aldehyde dehydrogenase is the second enzyme of the major oxidative pathway of alcohol metabolism. Two major liver isoforms of aldehyde dehydrogenase, cytosolic and mitochondrial, can be distinguished by their electrophoretic mobilities, kinetic properties, and subcellular localizations. Most Caucasians have two major isozymes, while approximately 50% of East Asians have the cytosolic isozyme but not the mitochondrial isozyme. A remarkably higher frequency of acute alcohol intoxication among East Asians than among Caucasians could be related to the absence of a catalytically active form of the mitochondrial isozyme. The increased exposure to acetaldehyde in individuals with the catalytically inactive form may also confer greater susceptibility to many types of cancer. This gene encodes a mitochondrial isoform, which has a low Km for acetaldehydes, and is localized in mitochondrial matrix. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH2	NM_000690.4	c.1522-393C>G		intron_variant		ENST00000261733.7
ALDH2	NM_001204889.2	c.1381-393C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH2	ENST00000261733.7	c.1522-393C>G		intron_variant		1	NM_000690.4	P1
ALDH2	ENST00000416293.7	c.1381-393C>G		intron_variant		2
ALDH2	ENST00000548536.1	c.*1398-393C>G		intron_variant, NMD_transcript_variant		3
ALDH2	ENST00000549106.1	c.*101-393C>G		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53515 AN: 151952 Hom.: 13854 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.353 AC: 53617 AN: 152070 Hom.: 13895 Cov.: 32 AF XY: 0.353 AC XY: 26231 AN XY: 74344

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.331

Alfa AF: 0.106 Hom.: 148

Bravo AF: 0.387

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.1
Dann	Benign	0.71

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: rs7296651; hg19: chr12-112246954;