19-41479716-T-C

Variant names:

• chr19-41479716-T-C
• rs887391
• ENST00000588495.6:n.950-432A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	n.955-432A>G		intron_variant	Intron 2 of 3
PCAT19	NR_136334.1	n.67-432A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT19	ENST00000588495.6	n.950-432A>G		intron_variant	Intron 2 of 3	1
PCAT19	ENST00000594315.3	n.171-432A>G		intron_variant	Intron 2 of 3	1
PCAT19	ENST00000595837.1	n.61+20868A>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47229 AN: 151842 Hom.: 8637 Cov.: 32

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.: 32 AF XY: 0.309 AC XY: 22934 AN XY: 74262

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.298

Alfa AF: 0.250 Hom.: 2782

Bravo AF: 0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887391; hg19: -;