19-41479679-G-A

Position:

• chr19-41479679-G-A

Variant summary

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

The NR_136334.1(PCAT19):​n.67-395C>T variant causes a intron, non coding transcript 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 NR_136334.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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=1.892).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCAT19	NR_136334.1	n.67-395C>T		intron_variant, non_coding_transcript_variant
PCAT19	NR_040109.2	n.955-395C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT19	ENST00000652333.1	n.62-395C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.361

Alfa AF: 0.281 Hom.: 6712

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11672691; hg19: -;