ENST00000579964.6:n.92+26123T>G

Variant names:

• chr18-26681957-T-G
• rs8083994
• ENST00000579964.6:n.92+26123T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000579964.6(AQP4-AS1):​n.92+26123T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,036 control chromosomes in the GnomAD database, including 19,546 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 0.50 (19546 hom., cov: 32)
• Consequence: AQP4-AS1 ENST00000579964.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102725227	XR_935311.4	n.105-6122T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP4-AS1	ENST00000579964.6	n.92+26123T>G		intron_variant	Intron 1 of 4	5
AQP4-AS1	ENST00000582605.5	n.93+26123T>G		intron_variant	Intron 1 of 5	4
AQP4-AS1	ENST00000583852.2	n.96-6122T>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76330 AN: 151920 Hom.: 19544 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.502 AC: 76370 AN: 152036 Hom.: 19546 Cov.: 32 AF XY: 0.496 AC XY: 36826 AN XY: 74308

African (AFR) AF: 0.441 AC: 18299 AN: 41458

American (AMR) AF: 0.443 AC: 6773 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1752 AN: 5182

South Asian (SAS) AF: 0.428 AC: 2059 AN: 4814

European-Finnish (FIN) AF: 0.505 AC: 5324 AN: 10550

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38262 AN: 67962

Other (OTH) AF: 0.486 AC: 1028 AN: 2114

Alfa AF: 0.537 Hom.: 72820

Bravo AF: 0.497

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	21
DANN	Benign	0.73
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs8083994; hg19: chr18-24261921;