chr8-127081233-C-T

Position:

• chr8-127081233-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.1360C>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 0.557 in 151,676 control chromosomes in the GnomAD database, including 24,219 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 0.56 (24219 hom., cov: 33)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

PRNCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.1360C>T		non_coding_transcript_exon_variant	1/1
PCAT2	NR_119373.1	n.101+888G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.1360C>T		non_coding_transcript_exon_variant	1/1	6
CASC19	ENST00000523510.1	n.101+888G>A		intron_variant		3
CASC19	ENST00000641794.1	n.162+888G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84378 AN: 151548 Hom.: 24195 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.557 AC: 84445 AN: 151668 Hom.: 24219 Cov.: 33 AF XY: 0.546 AC XY: 40483 AN XY: 74120

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.541

Alfa AF: 0.515 Hom.: 12121

Bravo AF: 0.561

Asia WGS AF: 0.480 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551510; hg19: chr8-128093478;