chr11-68008772-G-A

Position:

• chr11-68008772-G-A

Variant summary

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

The NM_001161473.3(ALDH3B1):​c.-2+80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,220 control chromosomes in the GnomAD database, including 19,059 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 0.49 (19050 hom., cov: 34)
  • Exomes 𝑓: 0.41 (9 hom.)
• Consequence: ALDH3B1 NM_001161473.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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

Verdict is Benign. Variant got -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 = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH3B1	NM_001161473.3	c.-2+80G>A		intron_variant			NP_001154945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH3B1	ENST00000614849.4	c.-2+80G>A		intron_variant		1		ENSP00000478486.1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74752 AN: 152004 Hom.: 19022 Cov.: 34

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.466

GnomAD4 exome AF: 0.408 AC: 40 AN: 98 Hom.: 9 AF XY: 0.394 AC XY: 26 AN XY: 66

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.492 AC: 74831 AN: 152122 Hom.: 19050 Cov.: 34 AF XY: 0.486 AC XY: 36126 AN XY: 74366

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.462

Alfa AF: 0.454 Hom.: 18592

Bravo AF: 0.494

Asia WGS AF: 0.397 AC: 1381 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	1.7
DANN	Benign	0.84

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: rs308338; hg19: chr11-67776242;