3-151789962-C-T

Variant names:

• chr3-151789962-C-T
• rs1401970
• ENST00000475855.1:n.320-15297G>A

Variant summary

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

The NR_110202.1(AADACL2-AS1):​n.320-15297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,064 control chromosomes in the GnomAD database, including 2,048 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 0.16 (2048 hom., cov: 32)
• Consequence: AADACL2-AS1 NR_110202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962
• Publications: 3 publications found

Genes affected

AADACL2-AS1 (HGNC:50301): (AADACL2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_110202.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AADACL2-AS1	NR_110202.1		n.320-15297G>A		intron	N/A
	AADACL2-AS1	NR_110203.1		n.320-15297G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AADACL2-AS1	ENST00000475855.1	TSL:5	n.320-15297G>A		intron	N/A
	AADACL2-AS1	ENST00000483843.6	TSL:5	n.440-15297G>A		intron	N/A
	AADACL2-AS1	ENST00000754423.1		n.323-15297G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24096 AN: 151946 Hom.: 2040 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.159 AC: 24124 AN: 152064 Hom.: 2048 Cov.: 32 AF XY: 0.157 AC XY: 11642 AN XY: 74340

African (AFR) AF: 0.115 AC: 4751 AN: 41492

American (AMR) AF: 0.181 AC: 2760 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5170

South Asian (SAS) AF: 0.188 AC: 904 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1234 AN: 10560

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11888 AN: 67966

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.172 Hom.: 3949

Bravo AF: 0.163

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs1401970; hg19: chr3-151507750;