12-69991543-C-T

Position:

• chr12-69991543-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69991543C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRANCR	ENST00000549419.6	n.153-87124G>A		intron_variant		4
PRANCR	ENST00000668518.1	n.370-87124G>A		intron_variant

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.246

Alfa AF: 0.249 Hom.: 6598

Bravo AF: 0.235

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882191; hg19: chr12-70385323;