17-19667007-A-G

Variant names:

• chr17-19667007-A-G
• rs8069576
• NM_000382.3:c.1207+1960A>G

Variant summary

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

The NM_000382.3(ALDH3A2):​c.1207+1960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,710 control chromosomes in the GnomAD database, including 25,866 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 0.58 (25866 hom., cov: 31)
• Consequence: ALDH3A2 NM_000382.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

Genes affected

ALDH3A2 (HGNC:403): (aldehyde dehydrogenase 3 family member A2) Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3A2	NM_000382.3	c.1207+1960A>G		intron_variant	Intron 8 of 9	ENST00000176643.11	NP_000373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH3A2	ENST00000176643.11	c.1207+1960A>G		intron_variant	Intron 8 of 9	1	NM_000382.3	ENSP00000176643.6

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87380 AN: 151594 Hom.: 25828 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.577 AC: 87467 AN: 151710 Hom.: 25866 Cov.: 31 AF XY: 0.582 AC XY: 43162 AN XY: 74122

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.581

Alfa AF: 0.563 Hom.: 23032

Bravo AF: 0.586

Asia WGS AF: 0.828 AC: 2869 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.78

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: rs8069576; hg19: chr17-19570320; COSMIC: COSV51568466; COSMIC: COSV51568466;