rs16834898

Positions:

• chr2-192772562-A-C
• chr2-192772562-A-G
• chr2-192772562-A-T

Variant summary

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

The NR_152587.1(PCGEM1):​n.391-3016A>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 0.525 in 151,992 control chromosomes in the GnomAD database, including 21,370 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 0.52 (21370 hom., cov: 33)
• Consequence: PCGEM1 NR_152587.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

PCGEM1 (HGNC:30145): (PCGEM1 prostate-specific transcript) This gene produces a long non-coding RNA that is overexpressed in prostate cancer and may act a marker for tumor progression. This RNA may act a negative regulator of apoptosis, and may promote activity of androgen receptor and Myc. [provided by RefSeq, Dec 2017]

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 (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGEM1	NR_152587.1	n.391-3016A>C		intron_variant, non_coding_transcript_variant
PCGEM1	NR_002769.1	n.269-3016A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGEM1	ENST00000454040.5	n.269-3016A>C		intron_variant, non_coding_transcript_variant		1
PCGEM1	ENST00000606314.1	n.269-3016A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79651 AN: 151874 Hom.: 21346 Cov.: 33

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.525 AC: 79721 AN: 151992 Hom.: 21370 Cov.: 33 AF XY: 0.521 AC XY: 38715 AN XY: 74272

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.516

Alfa AF: 0.346 Hom.: 847

Bravo AF: 0.525

Asia WGS AF: 0.575 AC: 1997 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16834898; hg19: chr2-193637288;