18-26827981-G-A

Position:

• chr18-26827981-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.93-96779G>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 0.294 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP4-AS1	ENST00000579964.6	n.93-96779G>A		intron_variant, non_coding_transcript_variant		5
AQP4-AS1	ENST00000582605.5	n.306-96779G>A		intron_variant, non_coding_transcript_variant		4
AQP4-AS1	ENST00000627963.2	n.193+63650G>A		intron_variant, non_coding_transcript_variant		5
AQP4-AS1	ENST00000628174.2	n.822+63650G>A		intron_variant, non_coding_transcript_variant		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;