12-72913802-A-G

Position:

• chr12-72913802-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 0.243 in 151,874 control chromosomes in the GnomAD database, including 4,644 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 (4644 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72913802A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36927 AN: 151756 Hom.: 4633 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.243 AC: 36971 AN: 151874 Hom.: 4644 Cov.: 32 AF XY: 0.241 AC XY: 17925 AN XY: 74232

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.217

Alfa AF: 0.232 Hom.: 2053

Bravo AF: 0.244

Asia WGS AF: 0.187 AC: 653 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.092
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10879517; hg19: chr12-73307582;