12-63056902-A-G

Position:

• chr12-63056902-A-G

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 0.354 in 151,888 control chromosomes in the GnomAD database, including 9,803 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 0.35 (9803 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63056902A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53740 AN: 151768 Hom.: 9800 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.354 AC: 53750 AN: 151888 Hom.: 9803 Cov.: 31 AF XY: 0.357 AC XY: 26492 AN XY: 74216

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.365

Alfa AF: 0.391 Hom.: 15819

Bravo AF: 0.350

Asia WGS AF: 0.357 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3913039; hg19: chr12-63450682;