ENST00000549419.6:n.153-161280C>A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902959	XR_007063359.1	n.192+1085G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRANCR	ENST00000549419.6	n.153-161280C>A		intron_variant	Intron 2 of 2	4
PRANCR	ENST00000668518.1	n.370-161280C>A		intron_variant	Intron 2 of 2
ENSG00000306323	ENST00000816977.1	n.81+1085G>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs4761289; hg19: chr12-70459479;