rs527616

Variant names:

• chr18-26757460-C-G
• rs527616
• ENST00000579964.6:n.92+101626C>G

Your query was ambiguous. Multiple possible variants found:

• chr18-26757460-C-G
• chr18-26757460-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000582605.5(AQP4-AS1):​n.305+47421C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,120 control chromosomes in the GnomAD database, including 39,248 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 0.71 (39248 hom., cov: 32)
• Consequence: AQP4-AS1 ENST00000582605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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.92+101626C>G		intron_variant	Intron 1 of 4	5
AQP4-AS1	ENST00000582605.5	n.305+47421C>G		intron_variant	Intron 3 of 5	4
AQP4-AS1	ENST00000628174.2	n.707-6756C>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107558 AN: 152002 Hom.: 39184 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.708 AC: 107684 AN: 152120 Hom.: 39248 Cov.: 32 AF XY: 0.706 AC XY: 52460 AN XY: 74348

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.703

Alfa AF: 0.658 Hom.: 4249

Bravo AF: 0.734

Asia WGS AF: 0.767 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	19
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs527616; hg19: chr18-24337424;