rs4406477

chr9-73037542-C-T

Variant summary

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

The ENST00000419959.5(ALDH1A1):c.-15+42825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,044 control chromosomes in the GnomAD database, including 25,192 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 0.57 (25192 hom., cov: 32)
• Consequence: ALDH1A1 ENST00000419959.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

ALDH1A1 (HGNC:402): (aldehyde dehydrogenase 1 family member A1) The protein encoded by this gene belongs to the aldehyde dehydrogenase family. Aldehyde dehydrogenase is the next enzyme after alcohol dehydrogenase in the major pathway of alcohol metabolism. There are two major aldehyde dehydrogenase isozymes in the liver, cytosolic and mitochondrial, which are encoded by distinct genes, and can be distinguished by their electrophoretic mobility, kinetic properties, and subcellular localization. This gene encodes the cytosolic isozyme. Studies in mice show that through its role in retinol metabolism, this gene may also be involved in the regulation of the metabolic responses to high-fat diet. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH1A1	ENST00000419959.5	c.-15+42825G>A		intron_variant		5
ALDH1A1	ENST00000446946.1	c.-15+999G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86834 AN: 151924 Hom.: 25162 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.572 AC: 86912 AN: 152044 Hom.: 25192 Cov.: 32 AF XY: 0.575 AC XY: 42705 AN XY: 74316

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.581

Alfa AF: 0.581 Hom.: 3160

Bravo AF: 0.562

Asia WGS AF: 0.469 AC: 1634 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.80
Dann	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4406477; hg19: chr9-75652458;