Genetic Variant NM_005672.5:c.*551C>G (chr8-142682683-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00800

Publications

14 publications found

Variant links:

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]

PSCA links:

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ACMG classification

Classification was made for transcript

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

Selected	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
	PSCA	NR_033343.2		n.1143C>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PSCA	ENST00000301258.5	TSL:1 MANE Select	c.*551C>G	3_prime_UTR	Exon 3 of 3	ENSP00000301258.4
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.:

show subpopulations

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.:

AF XY:

0.447

AC XY:

45902

AN XY:

102738

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

2049

4099

6148

8198

10247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

334

668

1002

1336

1670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.442

AC:

67160

AN:

151992

Hom.:

14993

Cov.:

AF XY:

0.442

AC XY:

32869

AN XY:

74290

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1973

3946

5918

7891

9864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.52

PhyloP100

0.0080

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over