rs4761285

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-70058183-G-A
• chr12-70058183-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 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.153-153764C>T		intron_variant	Intron 2 of 2	4
PRANCR	ENST00000668518.1	n.370-153764C>T		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.0633

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0833

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0694 Hom.: 227

Bravo AF: 0.0888

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4761285; hg19: chr12-70451963;