rs11069062

Variant names:

• chr12-118725274-G-A
• rs11069062

Your query was ambiguous. Multiple possible variants found:

• chr12-118725274-G-A
• chr12-118725274-G-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 0.251 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

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 = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.237

Alfa AF: 0.246 Hom.: 1083

Bravo AF: 0.243

Asia WGS AF: 0.299 AC: 1038 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	9.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11069062; hg19: chr12-119163079;