rs9653034

Variant names:

• chr18-26659790-G-A
• rs9653034
• ENST00000579964.6:n.92+3956G>A

Variant summary

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

The ENST00000583852.2(AQP4-AS1):​n.95+3956G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,020 control chromosomes in the GnomAD database, including 26,282 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 0.58 (26282 hom., cov: 33)
• Consequence: AQP4-AS1 ENST00000583852.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 0 publications found

Genes affected

AQP4-AS1 (HGNC:26399): (AQP4 antisense RNA 1)

PCAT18 (HGNC:49211): (prostate cancer associated transcript 18)

LOC102725227 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583852.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AQP4-AS1	ENST00000579964.6	TSL:5	n.92+3956G>A		intron	N/A
	AQP4-AS1	ENST00000582605.5	TSL:4	n.93+3956G>A		intron	N/A
	AQP4-AS1	ENST00000583852.2	TSL:3	n.95+3956G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88416 AN: 151902 Hom.: 26263 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.582 AC: 88482 AN: 152020 Hom.: 26282 Cov.: 33 AF XY: 0.573 AC XY: 42585 AN XY: 74298

African (AFR) AF: 0.654 AC: 27149 AN: 41482

American (AMR) AF: 0.508 AC: 7757 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2059 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2009 AN: 5164

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4814

European-Finnish (FIN) AF: 0.578 AC: 6089 AN: 10538

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39878 AN: 67960

Other (OTH) AF: 0.548 AC: 1156 AN: 2110

Alfa AF: 0.580 Hom.: 24614

Bravo AF: 0.586

Asia WGS AF: 0.340 AC: 1183 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.60
PhyloP100		-0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9653034;

hg19: chr18-24239754;