rs162004

Variant names:

• chr18-26867972-C-G
• rs162004
• ENST00000578701.5:n.54+2612C>G

Your query was ambiguous. Multiple possible variants found:

• chr18-26867972-C-G
• chr18-26867972-C-T

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+2612C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,106 control chromosomes in the GnomAD database, including 31,604 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 0.64 (31604 hom., cov: 32)
• Consequence: AQP4-AS1 ENST00000578701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP4-AS1	NR_026908.1	n.53+2612C>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP4-AS1	ENST00000578701.5	n.54+2612C>G		intron_variant	Intron 1 of 3	1
AQP4-AS1	ENST00000669364.1	n.19C>G		non_coding_transcript_exon_variant	Exon 1 of 8
AQP4-AS1	ENST00000568797.3	n.53+2612C>G		intron_variant	Intron 1 of 7	2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97945 AN: 151986 Hom.: 31573 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.644 AC: 98028 AN: 152106 Hom.: 31604 Cov.: 32 AF XY: 0.645 AC XY: 47942 AN XY: 74354

African (AFR) AF: 0.645 AC: 26749 AN: 41474

American (AMR) AF: 0.617 AC: 9436 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2373 AN: 3468

East Asian (EAS) AF: 0.662 AC: 3423 AN: 5172

South Asian (SAS) AF: 0.731 AC: 3523 AN: 4818

European-Finnish (FIN) AF: 0.633 AC: 6695 AN: 10572

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43785 AN: 67998

Other (OTH) AF: 0.654 AC: 1382 AN: 2114

Alfa AF: 0.535 Hom.: 1475

Bravo AF: 0.642

Asia WGS AF: 0.693 AC: 2412 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	2.4
DANN	Benign	0.38
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs162004; hg19: chr18-24447936;