rs6434568

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-192758626-C-A
• chr2-192758626-C-G
• chr2-192758626-C-T

Variant summary

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

The ENST00000454040.5(PCGEM1):​n.268+7754C>A variant causes a intron 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 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
PCGEM1	NR_002769.1	n.268+7754C>A		intron_variant	Intron 2 of 2
PCGEM1	NR_152587.1	n.390+4781C>A		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>A		intron_variant	Intron 2 of 2	1
PCGEM1	ENST00000606314.2	n.432+4781C>A		intron_variant	Intron 3 of 3	5
PCGEM1	ENST00000826526.1	n.268+4781C>A		intron_variant	Intron 3 of 3
PCGEM1	ENST00000826527.1	n.146+7754C>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.578 AC: 23971 AN: 41458

American (AMR) AF: 0.429 AC: 6531 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3466

East Asian (EAS) AF: 0.486 AC: 2494 AN: 5134

South Asian (SAS) AF: 0.516 AC: 2485 AN: 4814

European-Finnish (FIN) AF: 0.469 AC: 4947 AN: 10552

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31915 AN: 67862

Other (OTH) AF: 0.493 AC: 1040 AN: 2110

Alfa AF: 0.348 Hom.: 932

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
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;