12-70058183-G-A

Variant names:

• chr12-70058183-G-A
• rs4761285
• ENST00000549419.6:n.153-153764C>T

Variant summary

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

The ENST00000549419.6(PRANCR):​n.153-153764C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 152,160 control chromosomes in the GnomAD database, including 648 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 0.083 (648 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRANCR	ENST00000549419.6	TSL:4	n.153-153764C>T		intron	N/A
	PRANCR	ENST00000668518.1		n.370-153764C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12619 AN: 152044 Hom.: 647 Cov.: 32

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.0632

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0833

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0829 AC: 12618 AN: 152160 Hom.: 648 Cov.: 32 AF XY: 0.0845 AC XY: 6283 AN XY: 74388

African (AFR) AF: 0.0583 AC: 2421 AN: 41518

American (AMR) AF: 0.162 AC: 2473 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3468

East Asian (EAS) AF: 0.0533 AC: 276 AN: 5180

South Asian (SAS) AF: 0.0633 AC: 305 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1156 AN: 10578

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0833 AC: 5664 AN: 68002

Other (OTH) AF: 0.0863 AC: 182 AN: 2108

Alfa AF: 0.0702 Hom.: 252

Bravo AF: 0.0888

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.50
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4761285; hg19: chr12-70451963;