12-69998805-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549419.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRANCR	ENST00000549419.6	TSL:4	n.153-94386G>A		intron	N/A
	PRANCR	ENST00000668518.1		n.370-94386G>A		intron	N/A

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

African (AFR) AF: 0.229 AC: 9499 AN: 41470

American (AMR) AF: 0.353 AC: 5395 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2025 AN: 5160

South Asian (SAS) AF: 0.314 AC: 1510 AN: 4802

European-Finnish (FIN) AF: 0.371 AC: 3919 AN: 10554

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28662 AN: 67936

Other (OTH) AF: 0.363 AC: 764 AN: 2106

Alfa AF: 0.395 Hom.: 51534

Bravo AF: 0.347

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1152948;

hg19: chr12-70392585;