chr12-69991543-C-T

Variant names:

• chr12-69991543-C-T
• rs1882191
• ENST00000549419.6:n.153-87124G>A

Variant summary

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

The ENST00000549419.6(PRANCR):​n.153-87124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,078 control chromosomes in the GnomAD database, including 5,022 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 0.24 (5022 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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.153-87124G>A		intron	N/A
	PRANCR	ENST00000668518.1		n.370-87124G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36608 AN: 151958 Hom.: 5011 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.241 AC: 36631 AN: 152078 Hom.: 5022 Cov.: 32 AF XY: 0.251 AC XY: 18645 AN XY: 74334

African (AFR) AF: 0.125 AC: 5206 AN: 41498

American (AMR) AF: 0.328 AC: 5009 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2526 AN: 5166

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3787 AN: 10554

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16817 AN: 67982

Other (OTH) AF: 0.246 AC: 519 AN: 2112

Alfa AF: 0.248 Hom.: 8855

Bravo AF: 0.235

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs1882191; hg19: chr12-70385323;