19-41479716-T-C

Variant names:

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

Variant summary

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

The ENST00000652484.3(PCAT19):​n.61A>G variant causes a non coding transcript exon 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 ENST00000652484.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 48 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 (Cadd=3.592).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652484.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT19	NR_040109.2		n.955-432A>G		intron	N/A
	PCAT19	NR_136334.1		n.67-432A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT19	ENST00000588495.6	TSL:1	n.950-432A>G		intron	N/A
	PCAT19	ENST00000594315.4	TSL:1	n.173-432A>G		intron	N/A
	PCAT19	ENST00000595837.1	TSL:1	n.61+20868A>G		intron	N/A

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

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: 75 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15586 AN: 67968

Other (OTH) AF: 0.298 AC: 626 AN: 2104

Alfa AF: 0.248 Hom.: 3993

Bravo AF: 0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.6
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs887391;