rs6798928

Variant names:

• chr3-151862085-A-T
• rs6798928
• ENST00000475855.1:n.319+65772T>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.319+65772T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,952 control chromosomes in the GnomAD database, including 31,645 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 0.63 (31645 hom., cov: 31)
• Consequence: AADACL2-AS1 NR_110202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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.319+65772T>A		intron	N/A
	AADACL2-AS1	NR_110203.1		n.319+65772T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AADACL2-AS1	ENST00000475855.1	TSL:5	n.319+65772T>A		intron	N/A
	AADACL2-AS1	ENST00000483843.6	TSL:5	n.439+55530T>A		intron	N/A
	AADACL2-AS1	ENST00000754423.1		n.322+65772T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96288 AN: 151834 Hom.: 31594 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.634 AC: 96389 AN: 151952 Hom.: 31645 Cov.: 31 AF XY: 0.623 AC XY: 46250 AN XY: 74266

African (AFR) AF: 0.805 AC: 33376 AN: 41484

American (AMR) AF: 0.576 AC: 8781 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3466

East Asian (EAS) AF: 0.437 AC: 2252 AN: 5150

South Asian (SAS) AF: 0.455 AC: 2198 AN: 4830

European-Finnish (FIN) AF: 0.500 AC: 5274 AN: 10540

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40634 AN: 67926

Other (OTH) AF: 0.595 AC: 1254 AN: 2108

Alfa AF: 0.600 Hom.: 15312

Bravo AF: 0.647

Asia WGS AF: 0.470 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.65
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6798928; hg19: chr3-151579873;