3-126190132-C-A

Variant names:

• chr3-126190132-C-A
• rs13069815
• ENST00000500232.3:n.481+9588C>A

Variant summary

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

The ENST00000500232.3(ALDH1L1-AS2):​n.481+9588C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,220 control chromosomes in the GnomAD database, including 1,745 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 0.13 (1745 hom., cov: 32)
• Consequence: ALDH1L1-AS2 ENST00000500232.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 7 publications found

Genes affected

ALDH1L1-AS2 (HGNC:42446): (ALDH1L1 antisense RNA 2)

ALDH1L1 (HGNC:3978): (aldehyde dehydrogenase 1 family member L1) The protein encoded by this gene catalyzes the conversion of 10-formyltetrahydrofolate, nicotinamide adenine dinucleotide phosphate (NADP+), and water to tetrahydrofolate, NADPH, and carbon dioxide. The encoded protein belongs to the aldehyde dehydrogenase family. Loss of function or expression of this gene is associated with decreased apoptosis, increased cell motility, and cancer progression. There is an antisense transcript that overlaps on the opposite strand with this gene locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500232.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH1L1-AS2	NR_046383.1		n.480+9588C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH1L1-AS2	ENST00000500232.3	TSL:1	n.481+9588C>A		intron	N/A
	ALDH1L1	ENST00000509952.5	TSL:4	c.-24+7603G>T		intron	N/A	ENSP00000426594.1
	ALDH1L1-AS2	ENST00000502278.2	TSL:4	n.290+9767C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20420 AN: 152100 Hom.: 1739 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.134 AC: 20456 AN: 152220 Hom.: 1745 Cov.: 32 AF XY: 0.135 AC XY: 10041 AN XY: 74430

African (AFR) AF: 0.224 AC: 9283 AN: 41534

American (AMR) AF: 0.182 AC: 2784 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3468

East Asian (EAS) AF: 0.119 AC: 616 AN: 5186

South Asian (SAS) AF: 0.148 AC: 715 AN: 4826

European-Finnish (FIN) AF: 0.0557 AC: 591 AN: 10606

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0870 AC: 5916 AN: 68012

Other (OTH) AF: 0.133 AC: 280 AN: 2110

Alfa AF: 0.101 Hom.: 1520

Bravo AF: 0.146

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.74
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs13069815; hg19: chr3-125908975;