18-26893778-G-C

Variant names:

• chr18-26893778-G-C
• rs163061
• ENST00000578701.5:n.54+28418G>C

Variant summary

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

The ENST00000578701.5(AQP4-AS1):​n.54+28418G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,052 control chromosomes in the GnomAD database, including 35,864 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 0.68 (35864 hom., cov: 32)
• Consequence: AQP4-AS1 ENST00000578701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 1 publications found

Genes affected

AQP4-AS1 (HGNC:26399): (AQP4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578701.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQP4-AS1	NR_026908.1		n.175+786G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQP4-AS1	ENST00000578701.5	TSL:1	n.54+28418G>C		intron	N/A
	AQP4-AS1	ENST00000568797.3	TSL:2	n.175+786G>C		intron	N/A
	AQP4-AS1	ENST00000579964.6	TSL:5	n.93-30982G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103557 AN: 151934 Hom.: 35846 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.681 AC: 103614 AN: 152052 Hom.: 35864 Cov.: 32 AF XY: 0.683 AC XY: 50755 AN XY: 74338

African (AFR) AF: 0.551 AC: 22827 AN: 41432

American (AMR) AF: 0.692 AC: 10561 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2700 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3457 AN: 5174

South Asian (SAS) AF: 0.632 AC: 3044 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8204 AN: 10582

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50499 AN: 67984

Other (OTH) AF: 0.694 AC: 1464 AN: 2110

Alfa AF: 0.703 Hom.: 4730

Bravo AF: 0.672

Asia WGS AF: 0.569 AC: 1978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.28
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs163061; hg19: chr18-24473742;