rs4800770

Variant names:

• chr18-26827981-G-A
• rs4800770
• ENST00000579964.6:n.93-96779G>A

Variant summary

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

The ENST00000582605.5(AQP4-AS1):​n.306-96779G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,072 control chromosomes in the GnomAD database, including 7,571 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 0.29 (7571 hom., cov: 32)
• Consequence: AQP4-AS1 ENST00000582605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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.93-96779G>A		intron_variant	Intron 1 of 4	5
AQP4-AS1	ENST00000582605.5	n.306-96779G>A		intron_variant	Intron 3 of 5	4
AQP4-AS1	ENST00000627963.2	n.193+63650G>A		intron_variant	Intron 1 of 3	5
AQP4-AS1	ENST00000628174.2	n.822+63650G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44692 AN: 151954 Hom.: 7560 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.294 AC: 44717 AN: 152072 Hom.: 7571 Cov.: 32 AF XY: 0.294 AC XY: 21823 AN XY: 74322

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.321

Alfa AF: 0.315 Hom.: 979

Bravo AF: 0.300

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800770; hg19: chr18-24407945;