12-69998805-C-T

Variant names:

• chr12-69998805-C-T
• rs1152948
• ENST00000549419.6:n.153-94386G>A

Variant summary

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

The ENST00000549419.6(PRANCR):​n.153-94386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,984 control chromosomes in the GnomAD database, including 9,833 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 0.35 (9833 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 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.153-94386G>A		intron_variant	Intron 2 of 2	4
PRANCR	ENST00000668518.1	n.370-94386G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53182 AN: 151866 Hom.: 9837 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.350 AC: 53184 AN: 151984 Hom.: 9833 Cov.: 32 AF XY: 0.344 AC XY: 25580 AN XY: 74274

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.363

Alfa AF: 0.398 Hom.: 25237

Bravo AF: 0.347

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1152948; hg19: chr12-70392585;