NM_005672.5:c.*551C>G

Variant names:

• chr8-142682683-C-G
• rs1045605
• NM_005672.5:c.*551C>G

Variant summary

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

The NM_005672.5(PSCA):​c.*551C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 341,810 control chromosomes in the GnomAD database, including 34,370 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 0.44 (14993 hom., cov: 32)
  • Exomes 𝑓: 0.45 (19377 hom.)
• Consequence: PSCA NM_005672.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 14 publications found

Genes affected

PSCA (HGNC:9500): (prostate stem cell antigen) This gene encodes a glycosylphosphatidylinositol-anchored cell membrane glycoprotein. In addition to being highly expressed in the prostate it is also expressed in the bladder, placenta, colon, kidney, and stomach. This gene is up-regulated in a large proportion of prostate cancers and is also detected in cancers of the bladder and pancreas. This gene includes a polymorphism that results in an upstream start codon in some individuals; this polymorphism is thought to be associated with a risk for certain gastric and bladder cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

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 (AMR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005672.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSCA	NM_005672.5	MANE Select	c.*551C>G		3_prime_UTR	Exon 3 of 3	NP_005663.2	O43653
	PSCA	NR_033343.2		n.1143C>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSCA	ENST00000301258.5	TSL:1 MANE Select	c.*551C>G		3_prime_UTR	Exon 3 of 3	ENSP00000301258.4	O43653
	PSCA	ENST00000918921.1		c.*551C>G		3_prime_UTR	Exon 4 of 4	ENSP00000588980.1
	PSCA	ENST00000966863.1		c.*551C>G		downstream_gene	N/A	ENSP00000636922.1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67094 AN: 151874 Hom.: 14966 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.441

GnomAD4 exome AF: 0.447 AC: 84909 AN: 189818 Hom.: 19377 Cov.: 0 AF XY: 0.447 AC XY: 45902 AN XY: 102738

African (AFR) AF: 0.381 AC: 1955 AN: 5136

American (AMR) AF: 0.533 AC: 5840 AN: 10954

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 2205 AN: 4346

East Asian (EAS) AF: 0.324 AC: 2620 AN: 8086

South Asian (SAS) AF: 0.443 AC: 17293 AN: 39066

European-Finnish (FIN) AF: 0.499 AC: 4213 AN: 8438

Middle Eastern (MID) AF: 0.473 AC: 546 AN: 1154

European-Non Finnish (NFE) AF: 0.445 AC: 46058 AN: 103420

Other (OTH) AF: 0.453 AC: 4179 AN: 9218

GnomAD4 genome AF: 0.442 AC: 67160 AN: 151992 Hom.: 14993 Cov.: 32 AF XY: 0.442 AC XY: 32869 AN XY: 74290

African (AFR) AF: 0.389 AC: 16129 AN: 41444

American (AMR) AF: 0.512 AC: 7821 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1791 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1800 AN: 5136

South Asian (SAS) AF: 0.416 AC: 2005 AN: 4824

European-Finnish (FIN) AF: 0.508 AC: 5378 AN: 10588

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30810 AN: 67942

Other (OTH) AF: 0.443 AC: 934 AN: 2106

Alfa AF: 0.337 Hom.: 990

Bravo AF: 0.439

Asia WGS AF: 0.407 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.52
PhyloP100		0.0080
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1045605; hg19: chr8-143764101; COSMIC: COSV56652860; COSMIC: COSV56652860;