dbSNP rs2976396: PSCA:c.*451G>A (chr8-142682583-G-A) – 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.*451G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 375,438 control chromosomes in the GnomAD database, including 38,492 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 ( 14965 hom., cov: 33)

Exomes 𝑓: 0.45 ( 23527 hom. )

Consequence

PSCA
NM_005672.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

24 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:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSCA	NM_005672.5 link	c.*451G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000301258.5	NP_005663.2	O43653D3DWI6
PSCA	NR_033343.2 link	n.1043G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSCA	ENST00000301258.5 link	c.*451G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_005672.5	ENSP00000301258.4		O43653

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67059

AN:

151936

Hom.:

14938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.352

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.442

GnomAD2 exomes

AF:

0.447

AC:

30789

AN:

68864

AF XY:

0.445

show subpopulations

Gnomad AFR exome

AF:

0.374

Gnomad AMR exome

AF:

0.549

Gnomad ASJ exome

AF:

0.511

Gnomad EAS exome

AF:

0.312

Gnomad FIN exome

AF:

0.503

Gnomad NFE exome

AF:

0.447

Gnomad OTH exome

AF:

0.451

GnomAD4 exome

AF:

0.454

AC:

101512

AN:

223382

Hom.:

23527

Cov.:

AF XY:

0.454

AC XY:

55263

AN XY:

121856

show subpopulations

African (AFR)

AF:

0.381

AC:

2425

AN:

6368

American (AMR)

AF:

0.546

AC:

8440

AN:

15468

Ashkenazi Jewish (ASJ)

AF:

0.508

AC:

2766

AN:

5448

East Asian (EAS)

AF:

0.335

AC:

2881

AN:

8606

South Asian (SAS)

AF:

0.451

AC:

20934

AN:

46430

European-Finnish (FIN)

AF:

0.499

AC:

4725

AN:

9464

Middle Eastern (MID)

AF:

0.500

AC:

1178

AN:

2356

European-Non Finnish (NFE)

AF:

0.449

AC:

53207

AN:

118372

Other (OTH)

AF:

0.456

AC:

4956

AN:

10870

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

2543

5086

7628

10171

12714

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

408

816

1224

1632

2040

<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:

0.441

AC:

67125

AN:

152056

Hom.:

14965

Cov.:

AF XY:

0.442

AC XY:

32854

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.388

AC:

16110

AN:

41488

American (AMR)

AF:

0.511

AC:

7813

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

1795

AN:

3470

East Asian (EAS)

AF:

0.352

AC:

1815

AN:

5162

South Asian (SAS)

AF:

0.415

AC:

1995

AN:

4806

European-Finnish (FIN)

AF:

0.507

AC:

5368

AN:

10584

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.453

AC:

30801

AN:

67948

Other (OTH)

AF:

0.444

AC:

935

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1984

3968

5953

7937

9921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.451

Hom.:

17181

Bravo

AF:

0.438

Asia WGS

AF:

0.406

AC:

1411

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.6

(source)

DANN

Benign

0.41

PhyloP100

-0.097

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over