rs162004

Positions:

• chr18-26867972-C-G
• chr18-26867972-C-T

Variant summary

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

The NR_026908.1(AQP4-AS1):​n.53+2612C>G 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 0.644 in 152,106 control chromosomes in the GnomAD database, including 31,604 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 0.64 (31604 hom., cov: 32)
• Consequence: AQP4-AS1 NR_026908.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP4-AS1	NR_026908.1	n.53+2612C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP4-AS1	ENST00000578701.5	n.54+2612C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97945 AN: 151986 Hom.: 31573 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.644 AC: 98028 AN: 152106 Hom.: 31604 Cov.: 32 AF XY: 0.645 AC XY: 47942 AN XY: 74354

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.654

Alfa AF: 0.535 Hom.: 1475

Bravo AF: 0.642

Asia WGS AF: 0.693 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs162004; hg19: chr18-24447936;