ENST00000454040.5:n.268+7754C>T

Variant names:

• chr2-192758626-C-T
• rs6434568
• ENST00000454040.5:n.268+7754C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000454040.5(PCGEM1):​n.268+7754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 151,870 control chromosomes in the GnomAD database, including 1 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 0.0012 (1 hom., cov: 32)
• Consequence: PCGEM1 ENST00000454040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 14 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGEM1	NR_002769.1	n.268+7754C>T		intron_variant	Intron 2 of 2
PCGEM1	NR_152587.1	n.390+4781C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCGEM1	ENST00000454040.5	n.268+7754C>T		intron_variant	Intron 2 of 2	1
PCGEM1	ENST00000606314.2	n.432+4781C>T		intron_variant	Intron 3 of 3	5
PCGEM1	ENST00000826526.1	n.268+4781C>T		intron_variant	Intron 3 of 3
PCGEM1	ENST00000826527.1	n.146+7754C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00125 AC: 189 AN: 151752 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00406

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000295

Gnomad OTH AF: 0.000479

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

GnomAD4 genome AF: 0.00124 AC: 188 AN: 151870 Hom.: 1 Cov.: 32 AF XY: 0.00129 AC XY: 96 AN XY: 74218

African (AFR) AF: 0.00403 AC: 167 AN: 41476

American (AMR) AF: 0.00118 AC: 18 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5138

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000295 AC: 2 AN: 67876

Other (OTH) AF: 0.000474 AC: 1 AN: 2110

Alfa AF: 0.00 Hom.: 932

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs6434568; hg19: chr2-193623352;