chr12-30200961-A-G

Position:

• chr12-30200961-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 0.321 in 153,274 control chromosomes in the GnomAD database, including 11,897 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 0.32 (11873 hom., cov: 33)
  • Exomes 𝑓: 0.17 (24 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30200961A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257262	ENST00000549055.1	n.-22A>G		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48913 AN: 151958 Hom.: 11857 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.273

GnomAD4 exome AF: 0.170 AC: 204 AN: 1198 Hom.: 24 Cov.: 0 AF XY: 0.185 AC XY: 122 AN XY: 658

Gnomad4 AFR exome AF: 0.700

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.141

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.322 AC: 48969 AN: 152076 Hom.: 11873 Cov.: 33 AF XY: 0.325 AC XY: 24180 AN XY: 74350

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.272

Alfa AF: 0.215 Hom.: 1084

Bravo AF: 0.334

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1843321; hg19: chr12-30353894;