rs4374483

chr3-126201221-G-A

Variant summary

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

The NR_046383.1(ALDH1L1-AS2):n.481-7105G>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 0.428 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 NR_046383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH1L1-AS2	NR_046383.1	n.481-7105G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH1L1-AS2	ENST00000500232.3	n.482-7105G>A		intron_variant, non_coding_transcript_variant		1
ALDH1L1-AS2	ENST00000654154.2	n.534-7105G>A		intron_variant, non_coding_transcript_variant
ALDH1L1-AS2	ENST00000502278.1	n.291-7105G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.451

Alfa AF: 0.429 Hom.: 28470

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4374483; hg19: chr3-125920064;