chr19-41480023-T-A

Variant names:

• chr19-41480023-T-A
• rs11673591
• ENST00000588495.6:n.950-739A>T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 12 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588495.6. 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
	PCAT19	NR_040109.2		n.955-739A>T		intron	N/A
	PCAT19	NR_136334.1		n.67-739A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT19	ENST00000588495.6	TSL:1	n.950-739A>T		intron	N/A
	PCAT19	ENST00000594315.4	TSL:1	n.173-739A>T		intron	N/A
	PCAT19	ENST00000595837.1	TSL:1	n.61+20561A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62889 AN: 151886 Hom.: 17535 Cov.: 32

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.: 32 AF XY: 0.410 AC XY: 30459 AN XY: 74308

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: 86 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17421 AN: 67986

Other (OTH) AF: 0.362 AC: 762 AN: 2106

Alfa AF: 0.355 Hom.: 1568

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs11673591; hg19: chr19-41985931;