rs7851899

Variant names:

• chr9-72935759-G-A
• rs7851899
• NM_000689.5:c.171+4389C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-72935759-G-A
• chr9-72935759-G-T

Variant summary

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

The NM_000689.5(ALDH1A1):​c.171+4389C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,098 control chromosomes in the GnomAD database, including 61,857 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 0.90 (61857 hom., cov: 31)
• Consequence: ALDH1A1 NM_000689.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1A1	NM_000689.5	c.171+4389C>T		intron_variant	Intron 2 of 12	ENST00000297785.8	NP_000680.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1A1	ENST00000297785.8	c.171+4389C>T		intron_variant	Intron 2 of 12	1	NM_000689.5	ENSP00000297785.3

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136083 AN: 151980 Hom.: 61826 Cov.: 31

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.969

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.895 AC: 136171 AN: 152098 Hom.: 61857 Cov.: 31 AF XY: 0.897 AC XY: 66719 AN XY: 74348

African (AFR) AF: 0.723 AC: 29967 AN: 41450

American (AMR) AF: 0.947 AC: 14455 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2944 AN: 3468

East Asian (EAS) AF: 0.991 AC: 5124 AN: 5170

South Asian (SAS) AF: 0.910 AC: 4392 AN: 4826

European-Finnish (FIN) AF: 0.970 AC: 10282 AN: 10602

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.969 AC: 65917 AN: 68008

Other (OTH) AF: 0.912 AC: 1923 AN: 2108

Alfa AF: 0.925 Hom.: 98957

Bravo AF: 0.885

Asia WGS AF: 0.937 AC: 3256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		0.12
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: rs7851899; hg19: chr9-75550675;