12-69973851-C-T

Variant names:

• chr12-69973851-C-T
• rs1870419
• ENST00000549419.6:n.153-69432G>A

Variant summary

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

The ENST00000549419.6(PRANCR):​n.153-69432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,842 control chromosomes in the GnomAD database, including 3,101 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 0.19 (3101 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 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.153-69432G>A		intron_variant	Intron 2 of 2	4
PRANCR	ENST00000668518.1	n.370-69432G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28824 AN: 151726 Hom.: 3098 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.190 AC: 28824 AN: 151842 Hom.: 3101 Cov.: 32 AF XY: 0.189 AC XY: 14050 AN XY: 74236

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.212

Alfa AF: 0.197 Hom.: 1515

Bravo AF: 0.192

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870419; hg19: chr12-70367631;