12-118725274-G-A

Variant names:

• chr12-118725274-G-A
• rs11069062

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.251 in 151,918 control chromosomes in the GnomAD database, including 4,891 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 0.25 (4891 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.309 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38084 AN: 151800 Hom.: 4883 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.251 AC: 38123 AN: 151918 Hom.: 4891 Cov.: 31 AF XY: 0.251 AC XY: 18612 AN XY: 74250

African (AFR) AF: 0.314 AC: 12998 AN: 41416

American (AMR) AF: 0.165 AC: 2518 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1535 AN: 5108

South Asian (SAS) AF: 0.281 AC: 1353 AN: 4812

European-Finnish (FIN) AF: 0.230 AC: 2433 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15733 AN: 67958

Other (OTH) AF: 0.237 AC: 500 AN: 2112

Alfa AF: 0.237 Hom.: 6934

Bravo AF: 0.243

Asia WGS AF: 0.299 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.4
DANN	Benign	0.66
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs11069062; hg19: chr12-119163079;