rs9951307

Variant names:

• chr18-26850565-G-A
• rs9951307
• ENST00000579964.6:n.93-74195G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000582605.5(AQP4-AS1):​n.306-74195G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,048 control chromosomes in the GnomAD database, including 32,589 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 0.65 (32589 hom., cov: 32)
• Consequence: AQP4-AS1 ENST00000582605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP4-AS1	ENST00000579964.6	n.93-74195G>A		intron_variant	Intron 1 of 4	5
AQP4-AS1	ENST00000582605.5	n.306-74195G>A		intron_variant	Intron 3 of 5	4
AQP4-AS1	ENST00000627963.2	n.194-74195G>A		intron_variant	Intron 1 of 3	5
AQP4-AS1	ENST00000628174.2	n.823-74195G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99197 AN: 151932 Hom.: 32545 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.653 AC: 99300 AN: 152048 Hom.: 32589 Cov.: 32 AF XY: 0.655 AC XY: 48651 AN XY: 74306

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.673

Alfa AF: 0.658 Hom.: 67954

Bravo AF: 0.657

Asia WGS AF: 0.748 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.21
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9951307; hg19: chr18-24430529;