rs7043217

Variant names:

• chr9-72927979-G-A
• rs7043217
• NM_000689.5:c.443-802C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-72927979-G-A
• chr9-72927979-G-C
• chr9-72927979-G-T

Variant summary

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

The NM_000689.5(ALDH1A1):​c.443-802C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 136,762 control chromosomes in the GnomAD database, including 14,401 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 0.44 (14401 hom., cov: 24)
• Consequence: ALDH1A1 NM_000689.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1A1	NM_000689.5	c.443-802C>T		intron_variant	Intron 4 of 12	ENST00000297785.8	NP_000680.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1A1	ENST00000297785.8	c.443-802C>T		intron_variant	Intron 4 of 12	1	NM_000689.5	ENSP00000297785.3

Frequencies

GnomAD3 genomes AF: 0.441 AC: 60242 AN: 136658 Hom.: 14396 Cov.: 24

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.406

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.441 AC: 60286 AN: 136762 Hom.: 14401 Cov.: 24 AF XY: 0.441 AC XY: 29166 AN XY: 66118

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.443

Alfa AF: 0.512 Hom.: 17246

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.23

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: rs7043217; hg19: chr9-75542895;