rs13069815

Positions:

• chr3-126190132-C-A
• chr3-126190132-C-T

Variant summary

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

The NR_046383.1(ALDH1L1-AS2):​n.480+9588C>A variant causes a intron, non coding transcript 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 NR_046383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH1L1-AS2	NR_046383.1	n.480+9588C>A		intron_variant, non_coding_transcript_variant
ALDH1L1	XM_024453325.2	c.-24+7603G>T		intron_variant			XP_024309093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH1L1-AS2	ENST00000654154.2	n.533+9588C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.0453

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0950 Hom.: 1036

Bravo AF: 0.146

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13069815; hg19: chr3-125908975;