rs2017362

chr9-72929475-C-T

Variant summary

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

The NM_000689.5(ALDH1A1):c.313-454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,060 control chromosomes in the GnomAD database, including 9,789 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 0.36 (9789 hom., cov: 33)
• Consequence: ALDH1A1 NM_000689.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH1A1	NM_000689.5	c.313-454G>A		intron_variant		ENST00000297785.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH1A1	ENST00000297785.8	c.313-454G>A		intron_variant		1	NM_000689.5	P1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54111 AN: 151942 Hom.: 9792 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.356 AC: 54127 AN: 152060 Hom.: 9789 Cov.: 33 AF XY: 0.355 AC XY: 26385 AN XY: 74332

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.370

Alfa AF: 0.366 Hom.: 13535

Bravo AF: 0.361

Asia WGS AF: 0.464 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.94
Dann	Benign	0.31

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: rs2017362; hg19: chr9-75544391;