chr12-69973851-C-T

Position:

• chr12-69973851-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000549419.6(PRANCR):​n.153-69432G>A 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 0.19 in 151,842 control chromosomes in the GnomAD database, including 3,101 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 0.19 (3101 hom., cov: 32)
• Consequence: PRANCR ENST00000549419.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRANCR	ENST00000549419.6	n.153-69432G>A		intron_variant, non_coding_transcript_variant		4
PRANCR	ENST00000668518.1	n.370-69432G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28824 AN: 151726 Hom.: 3098 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.190 AC: 28824 AN: 151842 Hom.: 3101 Cov.: 32 AF XY: 0.189 AC XY: 14050 AN XY: 74236

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.212

Alfa AF: 0.197 Hom.: 1515

Bravo AF: 0.192

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870419; hg19: chr12-70367631;