12-69991543-C-T

Variant names:

• chr12-69991543-C-T
• rs1882191
• ENST00000549419.6:n.153-87124G>A

Variant summary

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

The ENST00000549419.6(PRANCR):​n.153-87124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,078 control chromosomes in the GnomAD database, including 5,022 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 0.24 (5022 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

PRANCR (HGNC:51126): (progenitor renewal associated non-coding RNA)

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 (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRANCR	ENST00000549419.6	n.153-87124G>A		intron_variant	Intron 2 of 2	4
PRANCR	ENST00000668518.1	n.370-87124G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36608 AN: 151958 Hom.: 5011 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.241

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.241 AC: 36631 AN: 152078 Hom.: 5022 Cov.: 32 AF XY: 0.251 AC XY: 18645 AN XY: 74334

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.246

Alfa AF: 0.249 Hom.: 6598

Bravo AF: 0.235

Asia WGS AF: 0.365 AC: 1269 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	3.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882191; hg19: chr12-70385323;