rs4800770

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579964.6(AQP4-AS1):​n.93-96779G>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 ENST00000579964.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579964.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQP4-AS1	ENST00000579964.6	TSL:5	n.93-96779G>A		intron	N/A
	AQP4-AS1	ENST00000582605.5	TSL:4	n.306-96779G>A		intron	N/A
	AQP4-AS1	ENST00000627963.2	TSL:5	n.193+63650G>A		intron	N/A

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

African (AFR) AF: 0.126 AC: 5224 AN: 41492

American (AMR) AF: 0.436 AC: 6657 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1809 AN: 5174

South Asian (SAS) AF: 0.387 AC: 1859 AN: 4806

European-Finnish (FIN) AF: 0.285 AC: 3018 AN: 10582

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24099 AN: 67956

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.309 Hom.: 995

Bravo AF: 0.300

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.33
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4800770; hg19: chr18-24407945;