Genetic Variant PCAT19:n.950-432A>G (chr19-41479716-T-C) – 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.950-432A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,960 control chromosomes in the GnomAD database, including 8,654 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 0.31 ( 8654 hom., cov: 32)

Consequence

PCAT19
ENST00000588495.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.622

Publications

48 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 (Cadd=3.592).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCAT19	NR_040109.2 link	n.955-432A>G		intron_variant	Intron 2 of 3
PCAT19	NR_136334.1 link	n.67-432A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PCAT19	ENST00000588495.6 link	n.950-432A>G	intron_variant	Intron 2 of 3	1
PCAT19	ENST00000594315.4 link	n.173-432A>G	intron_variant	Intron 2 of 3	1
PCAT19	ENST00000595837.1 link	n.61+20868A>G	intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47229

AN:

151842

Hom.:

8637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.252

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.295

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

GnomAD4 genome

AF:

0.311

AC:

47286

AN:

151960

Hom.:

8654

Cov.:

AF XY:

0.309

AC XY:

22934

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.499

AC:

20663

AN:

41394

American (AMR)

AF:

0.200

AC:

3052

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

868

AN:

3468

East Asian (EAS)

AF:

0.399

AC:

2063

AN:

5166

South Asian (SAS)

AF:

0.310

AC:

1498

AN:

4828

European-Finnish (FIN)

AF:

0.252

AC:

2656

AN:

10558

Middle Eastern (MID)

AF:

0.257

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.229

AC:

15586

AN:

67968

Other (OTH)

AF:

0.298

AC:

626

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1554

3108

4662

6216

7770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.248

Hom.:

3993

Bravo

AF:

0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

CADD

Benign

3.6

(source)

PhyloP100

-0.62

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