ENST00000454040.5:n.269-3016A>T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000454040.5(PCGEM1):​n.269-3016A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGEM1	NR_002769.1	n.269-3016A>T		intron_variant	Intron 2 of 2
PCGEM1	NR_152587.1	n.391-3016A>T		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>T		intron_variant	Intron 2 of 2	1
PCGEM1	ENST00000606314.2	n.433-3016A>T		intron_variant	Intron 3 of 3	5
PCGEM1	ENST00000826526.1	n.269-3019A>T		intron_variant	Intron 3 of 3
PCGEM1	ENST00000826527.1	n.147-3019A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 847

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	0.38
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;