chr8-127091724-C-T

Position:

• chr8-127091724-C-T

Variant summary

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

The NR_109833.1(PRNCR1):​n.11851C>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 0.258 in 151,982 control chromosomes in the GnomAD database, including 5,905 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 0.26 (5905 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

Genes affected

PRNCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.11851C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.11851C>T		non_coding_transcript_exon_variant	1/1	6
CASC19	ENST00000642100.1	n.418-12591G>A		intron_variant
PCAT1	ENST00000645463.1	n.855+85106C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39204 AN: 151864 Hom.: 5892 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.240

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.258 AC: 39270 AN: 151982 Hom.: 5905 Cov.: 32 AF XY: 0.261 AC XY: 19367 AN XY: 74288

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.246

Alfa AF: 0.222 Hom.: 506

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72725879; hg19: chr8-128103969; COSMIC: COSV73056813;