rs9951307

Positions:

• chr18-26850565-G-A

Variant summary

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

The ENST00000579964.6(AQP4-AS1):​n.93-74195G>A variant causes a intron, non coding transcript 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 ENST00000579964.6 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP4-AS1	ENST00000579964.6	n.93-74195G>A		intron_variant, non_coding_transcript_variant		5
AQP4-AS1	ENST00000582605.5	n.306-74195G>A		intron_variant, non_coding_transcript_variant		4
AQP4-AS1	ENST00000627963.2	n.194-74195G>A		intron_variant, non_coding_transcript_variant		5
AQP4-AS1	ENST00000628174.2	n.823-74195G>A		intron_variant, non_coding_transcript_variant		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;