rs506038

Positions:

• chr18-26691118-A-G

Variant summary

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

The NR_024259.1(PCAT18):​n.248-1147T>C 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 0.365 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 NR_024259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCAT18	NR_024259.1	n.248-1147T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT18	ENST00000579458.1	n.248-1147T>C		intron_variant, non_coding_transcript_variant		2
AQP4-AS1	ENST00000579964.6	n.92+35284A>G		intron_variant, non_coding_transcript_variant		5
AQP4-AS1	ENST00000582605.5	n.94-18332A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.333

Alfa AF: 0.258 Hom.: 9879

Bravo AF: 0.378

Asia WGS AF: 0.246 AC: 855 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs506038; hg19: chr18-24271082;