chr8-127081052-C-T

Position:

• chr8-127081052-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.1179C>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 0.203 in 152,162 control chromosomes in the GnomAD database, including 3,161 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 0.20 (3160 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

Genes affected

PRNCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.1179C>T		non_coding_transcript_exon_variant	1/1
PCAT2	NR_119373.1	n.101+1069G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.1179C>T		non_coding_transcript_exon_variant	1/1	6
CASC19	ENST00000523510.1	n.101+1069G>A		intron_variant		3
CASC19	ENST00000641794.1	n.162+1069G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30870 AN: 151932 Hom.: 3162 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.134 AC: 15 AN: 112 Hom.: 1 Cov.: 0 AF XY: 0.185 AC XY: 10 AN XY: 54

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.158

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.203 AC: 30877 AN: 152050 Hom.: 3160 Cov.: 32 AF XY: 0.202 AC XY: 15014 AN XY: 74334

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.179

Alfa AF: 0.205 Hom.: 7543

Bravo AF: 0.201

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.019
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016343; hg19: chr8-128093297;