18-26691118-A-G

Variant names:

• chr18-26691118-A-G
• rs506038
• ENST00000579458.2:n.393-1147T>C

Variant summary

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

The ENST00000579458.2(PCAT18):​n.393-1147T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,038 control chromosomes in the GnomAD database, including 12,777 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 0.36 (12777 hom., cov: 32)
• Consequence: PCAT18 ENST00000579458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

Genes affected

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

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579458.2. 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
	PCAT18	NR_024259.1		n.248-1147T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT18	ENST00000579458.2	TSL:2	n.393-1147T>C		intron	N/A
	AQP4-AS1	ENST00000579964.6	TSL:5	n.92+35284A>G		intron	N/A
	AQP4-AS1	ENST00000582605.5	TSL:4	n.94-18332A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55370 AN: 151920 Hom.: 12749 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.365 AC: 55456 AN: 152038 Hom.: 12777 Cov.: 32 AF XY: 0.363 AC XY: 26982 AN XY: 74296

African (AFR) AF: 0.664 AC: 27540 AN: 41460

American (AMR) AF: 0.307 AC: 4690 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3470

East Asian (EAS) AF: 0.143 AC: 736 AN: 5146

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4820

European-Finnish (FIN) AF: 0.319 AC: 3374 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16079 AN: 67968

Other (OTH) AF: 0.333 AC: 705 AN: 2116

Alfa AF: 0.284 Hom.: 22412

Bravo AF: 0.378

Asia WGS AF: 0.246 AC: 855 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.36
PhyloP100		-1.0

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: rs506038;

hg19: chr18-24271082;