rs13254738

Positions:

• chr8-127092098-C-A
• chr8-127092098-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.12225C>A 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 0.562 in 155,062 control chromosomes in the GnomAD database, including 26,115 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 (25535 hom., cov: 31)
  • Exomes 𝑓: 0.60 (580 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

Genes affected

PRNCR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.12225C>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.12225C>A		non_coding_transcript_exon_variant	1/1	6
CASC19	ENST00000642100.1	n.418-12965G>T		intron_variant
PCAT1	ENST00000645463.1	n.855+85480C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85329 AN: 151810 Hom.: 25545 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.585

GnomAD4 exome AF: 0.599 AC: 1877 AN: 3134 Hom.: 580 Cov.: 0 AF XY: 0.602 AC XY: 1001 AN XY: 1664

Gnomad4 AFR exome AF: 0.422

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.558

Gnomad4 EAS exome AF: 0.367

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.656

Gnomad4 NFE exome AF: 0.651

Gnomad4 OTH exome AF: 0.644

GnomAD4 genome AF: 0.562 AC: 85329 AN: 151928 Hom.: 25535 Cov.: 31 AF XY: 0.559 AC XY: 41513 AN XY: 74274

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.582

Alfa AF: 0.596 Hom.: 10149

Bravo AF: 0.539

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13254738; hg19: chr8-128104343;