12-70065699-G-T

Variant names:

• chr12-70065699-G-T
• rs4761289
• ENST00000549419.6:n.153-161280C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000549419.6(PRANCR):​n.153-161280C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,972 control chromosomes in the GnomAD database, including 15,087 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 0.44 (15087 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 2 publications found

Genes affected

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

ENSG00000306323 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.459 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.153-161280C>A		intron	N/A
	PRANCR	ENST00000668518.1		n.370-161280C>A		intron	N/A
	ENSG00000306323	ENST00000816977.1		n.81+1085G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67294 AN: 151856 Hom.: 15076 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.443 AC: 67357 AN: 151972 Hom.: 15087 Cov.: 32 AF XY: 0.442 AC XY: 32877 AN XY: 74304

African (AFR) AF: 0.462 AC: 19159 AN: 41436

American (AMR) AF: 0.468 AC: 7153 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2369 AN: 5164

South Asian (SAS) AF: 0.455 AC: 2193 AN: 4824

European-Finnish (FIN) AF: 0.496 AC: 5232 AN: 10546

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.423 AC: 28763 AN: 67940

Other (OTH) AF: 0.419 AC: 883 AN: 2108

Alfa AF: 0.367 Hom.: 1567

Bravo AF: 0.445

Asia WGS AF: 0.482 AC: 1675 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.83
PhyloP100		0.53

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: rs4761289;

hg19: chr12-70459479;