dbSNP rs11673591: PCAT19:n.950-739A>T (chr19-41480023-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000588495.6(PCAT19):n.950-739A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,006 control chromosomes in the GnomAD database, including 17,592 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 0.41 ( 17592 hom., cov: 32)

Consequence

PCAT19
ENST00000588495.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.841

Publications

12 publications found

Variant links:

Genes affected

PCAT19 (HGNC:49593): (prostate cancer associated transcript 19)

PCAT19 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCAT19	NR_040109.2 link	n.955-739A>T		intron_variant	Intron 2 of 3
PCAT19	NR_136334.1 link	n.67-739A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PCAT19	ENST00000588495.6 link	n.950-739A>T	intron_variant	Intron 2 of 3	1
PCAT19	ENST00000594315.4 link	n.173-739A>T	intron_variant	Intron 2 of 3	1
PCAT19	ENST00000595837.1 link	n.61+20561A>T	intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62889

AN:

151886

Hom.:

17535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.798

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.285

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.359

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

GnomAD4 genome

AF:

0.414

AC:

63006

AN:

152006

Hom.:

17592

Cov.:

AF XY:

0.410

AC XY:

30459

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.798

AC:

33025

AN:

41382

American (AMR)

AF:

0.240

AC:

3669

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

975

AN:

3470

East Asian (EAS)

AF:

0.415

AC:

2141

AN:

5154

South Asian (SAS)

AF:

0.348

AC:

1677

AN:

4822

European-Finnish (FIN)

AF:

0.285

AC:

3013

AN:

10582

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.256

AC:

17421

AN:

67986

Other (OTH)

AF:

0.362

AC:

762

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1460

2919

4379

5838

7298

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

538

1076

1614

2152

2690

<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:

0.355

Hom.:

1568

Bravo

AF:

0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.9

(source)

PhyloP100

-0.84

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over