rs16834898

Variant names:

• chr2-192772562-A-C
• rs16834898
• ENST00000454040.5:n.269-3016A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000454040.5(PCGEM1):​n.269-3016A>C variant causes a intron 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 ENST00000454040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 9 publications found

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

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 = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGEM1	NR_002769.1	n.269-3016A>C		intron_variant	Intron 2 of 2
PCGEM1	NR_152587.1	n.391-3016A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCGEM1	ENST00000454040.5	n.269-3016A>C		intron_variant	Intron 2 of 2	1
PCGEM1	ENST00000606314.2	n.433-3016A>C		intron_variant	Intron 3 of 3	5
PCGEM1	ENST00000826526.1	n.269-3019A>C		intron_variant	Intron 3 of 3
PCGEM1	ENST00000826527.1	n.147-3019A>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.640 AC: 26542 AN: 41458

American (AMR) AF: 0.454 AC: 6931 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3472

East Asian (EAS) AF: 0.493 AC: 2545 AN: 5166

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4810

European-Finnish (FIN) AF: 0.479 AC: 5049 AN: 10540

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32534 AN: 67962

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs16834898; hg19: chr2-193637288;