8-127080210-C-T

Position:

• chr8-127080210-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.337C>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 0.504 in 151,740 control chromosomes in the GnomAD database, including 20,023 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 0.50 (20023 hom., cov: 31)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

Genes affected

PRNCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.337C>T		non_coding_transcript_exon_variant	1/1
PCAT2	NR_119373.1	n.102-1077G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.337C>T		non_coding_transcript_exon_variant	1/1	6
CASC19	ENST00000523510.1	n.102-1077G>A		intron_variant		3
CASC19	ENST00000641794.1	n.163-1077G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76342 AN: 151616 Hom.: 20008 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.504 AC: 76400 AN: 151734 Hom.: 20023 Cov.: 31 AF XY: 0.495 AC XY: 36670 AN XY: 74112

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.491

Alfa AF: 0.468 Hom.: 13394

Bravo AF: 0.507

Asia WGS AF: 0.462 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016342; hg19: chr8-128092455;