rs308338

Variant names:

• chr11-68008772-G-A
• rs308338
• ENST00000614849.4:c.-2+80G>A

Variant summary

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

The ENST00000614849.4(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 ENST00000614849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• 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 = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3B1	NM_001161473.3	c.-2+80G>A		intron_variant	Intron 1 of 9		NP_001154945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH3B1	ENST00000614849.4	c.-2+80G>A		intron_variant	Intron 1 of 9	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.750 AC: 6 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.353 AC: 24 AN: 68

Other (OTH) AF: 0.500 AC: 5 AN: 10

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

African (AFR) AF: 0.622 AC: 25797 AN: 41488

American (AMR) AF: 0.393 AC: 6018 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1930 AN: 5162

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4528 AN: 10604

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31627 AN: 67950

Other (OTH) AF: 0.462 AC: 976 AN: 2114

Alfa AF: 0.459 Hom.: 24031

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
PhyloP100		-1.2
PromoterAI		-0.070	Neutral
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: rs308338; hg19: chr11-67776242;