chr19-41479679-G-A

Variant names:

• chr19-41479679-G-A
• rs11672691
• ENST00000588495.6:n.950-395C>T

Variant summary

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

The ENST00000652484.3(PCAT19):​n.98C>T 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 0.413 in 151,878 control chromosomes in the GnomAD database, including 17,497 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 (17497 hom., cov: 32)
• Consequence: PCAT19 ENST00000652484.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 117 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=1.892).
• 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: 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.955-395C>T		intron	N/A
	PCAT19	NR_136334.1		n.67-395C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT19	ENST00000588495.6	TSL:1	n.950-395C>T		intron	N/A
	PCAT19	ENST00000594315.4	TSL:1	n.173-395C>T		intron	N/A
	PCAT19	ENST00000595837.1	TSL:1	n.61+20905C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62584 AN: 151760 Hom.: 17445 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.413 AC: 62696 AN: 151878 Hom.: 17497 Cov.: 32 AF XY: 0.408 AC XY: 30280 AN XY: 74232

African (AFR) AF: 0.798 AC: 32991 AN: 41354

American (AMR) AF: 0.239 AC: 3650 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2146 AN: 5164

South Asian (SAS) AF: 0.338 AC: 1627 AN: 4810

European-Finnish (FIN) AF: 0.284 AC: 2992 AN: 10550

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17224 AN: 67964

Other (OTH) AF: 0.361 AC: 761 AN: 2106

Alfa AF: 0.316 Hom.: 28227

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.9
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11672691;