rs457860

Variant names:

• chr18-26878241-A-C
• rs457860
• ENST00000578701.5:n.54+12881A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-26878241-A-C
• chr18-26878241-A-G

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+12881A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,142 control chromosomes in the GnomAD database, including 68,854 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 0.95 (68854 hom., cov: 30)
• Consequence: AQP4-AS1 ENST00000578701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP4-AS1	NR_026908.1	n.53+12881A>C		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+12881A>C		intron_variant	Intron 1 of 3	1
AQP4-AS1	ENST00000568797.3	n.53+12881A>C		intron_variant	Intron 1 of 7	2
AQP4-AS1	ENST00000579964.6	n.93-46519A>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144591 AN: 152024 Hom.: 68789 Cov.: 30

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.951 AC: 144715 AN: 152142 Hom.: 68854 Cov.: 30 AF XY: 0.950 AC XY: 70634 AN XY: 74362

African (AFR) AF: 0.970 AC: 40245 AN: 41496

American (AMR) AF: 0.976 AC: 14921 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3343 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5156 AN: 5168

South Asian (SAS) AF: 0.945 AC: 4547 AN: 4814

European-Finnish (FIN) AF: 0.890 AC: 9412 AN: 10576

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.939 AC: 63872 AN: 68010

Other (OTH) AF: 0.960 AC: 2030 AN: 2114

Alfa AF: 0.945 Hom.: 8769

Bravo AF: 0.959

Asia WGS AF: 0.976 AC: 3394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.81
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs457860; hg19: chr18-24458205;