rs162007

Positions:

• chr18-26865883-G-A

Variant summary

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

The NR_026908.1(AQP4-AS1):​n.53+523G>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 0.204 in 614,086 control chromosomes in the GnomAD database, including 13,808 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 0.17 (2569 hom., cov: 33)
  • Exomes 𝑓: 0.21 (11239 hom.)
• Consequence: AQP4-AS1 NR_026908.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

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=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP4-AS1	NR_026908.1	n.53+523G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP4-AS1	ENST00000578701.5	n.54+523G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26477 AN: 151474 Hom.: 2575 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.194

GnomAD4 exome AF: 0.213 AC: 98650 AN: 462494 Hom.: 11239 AF XY: 0.219 AC XY: 53465 AN XY: 244314

Gnomad4 AFR exome AF: 0.104

Gnomad4 AMR exome AF: 0.133

Gnomad4 ASJ exome AF: 0.245

Gnomad4 EAS exome AF: 0.368

Gnomad4 SAS exome AF: 0.307

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.195

Gnomad4 OTH exome AF: 0.201

GnomAD4 genome AF: 0.175 AC: 26459 AN: 151592 Hom.: 2569 Cov.: 33 AF XY: 0.177 AC XY: 13106 AN XY: 74070

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.191

Alfa AF: 0.190 Hom.: 2724

Bravo AF: 0.164

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	20
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs162007; hg19: chr18-24445847;