3-126201221-G-A

Variant names:

• chr3-126201221-G-A
• rs4374483
• ENST00000500232.3:n.482-7105G>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.482-7105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,036 control chromosomes in the GnomAD database, including 14,125 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 0.43 (14125 hom., cov: 32)
• Consequence: ALDH1L1-AS2 ENST00000500232.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1L1-AS2	NR_046383.1	n.481-7105G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1L1-AS2	ENST00000500232.3	n.482-7105G>A		intron_variant	Intron 1 of 1	1
ALDH1L1-AS2	ENST00000502278.2	n.291-7105G>A		intron_variant	Intron 1 of 1	4
ALDH1L1-AS2	ENST00000654154.2	n.534-7105G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64963 AN: 151916 Hom.: 14126 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.428 AC: 65010 AN: 152036 Hom.: 14125 Cov.: 32 AF XY: 0.430 AC XY: 31932 AN XY: 74298

African (AFR) AF: 0.399 AC: 16534 AN: 41468

American (AMR) AF: 0.476 AC: 7280 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2797 AN: 5178

South Asian (SAS) AF: 0.339 AC: 1637 AN: 4822

European-Finnish (FIN) AF: 0.443 AC: 4675 AN: 10556

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29142 AN: 67940

Other (OTH) AF: 0.451 AC: 953 AN: 2114

Alfa AF: 0.427 Hom.: 44537

Bravo AF: 0.434

Asia WGS AF: 0.423 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.52
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4374483; hg19: chr3-125920064;