rs6434568

chr2-192758626-C-Achr2-192758626-C-Gchr2-192758626-C-T

Variant summary

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

The NR_152587.1(PCGEM1):n.390+4781C>A 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 0.499 in 151,814 control chromosomes in the GnomAD database, including 19,156 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 0.50 (19156 hom., cov: 32)
• Consequence: PCGEM1 NR_152587.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGEM1	NR_152587.1	n.390+4781C>A		intron_variant, non_coding_transcript_variant
PCGEM1	NR_002769.1	n.268+7754C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGEM1	ENST00000454040.5	n.268+7754C>A		intron_variant, non_coding_transcript_variant		1
PCGEM1	ENST00000606314.1	n.268+4781C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75717 AN: 151696 Hom.: 19138 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.499 AC: 75774 AN: 151814 Hom.: 19156 Cov.: 32 AF XY: 0.496 AC XY: 36822 AN XY: 74192

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.493

Alfa AF: 0.332 Hom.: 805

Bravo AF: 0.497

Asia WGS AF: 0.552 AC: 1918 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6434568; hg19: chr2-193623352;