rs4761285

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRANCR	ENST00000549419.6	n.153-153764C>T		intron_variant, non_coding_transcript_variant		4
PRANCR	ENST00000668518.1	n.370-153764C>T		intron_variant, non_coding_transcript_variant

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;