12-66186955-G-A

Variant names:

• chr12-66186955-G-A
• rs11176082

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 0.29 in 152,040 control chromosomes in the GnomAD database, including 6,851 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 0.29 (6851 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.403 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44091 AN: 151922 Hom.: 6844 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.290 AC: 44123 AN: 152040 Hom.: 6851 Cov.: 31 AF XY: 0.292 AC XY: 21682 AN XY: 74298

African (AFR) AF: 0.192 AC: 7950 AN: 41476

American (AMR) AF: 0.256 AC: 3915 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1792 AN: 5182

South Asian (SAS) AF: 0.418 AC: 2017 AN: 4820

European-Finnish (FIN) AF: 0.315 AC: 3324 AN: 10556

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22987 AN: 67958

Other (OTH) AF: 0.261 AC: 551 AN: 2110

Alfa AF: 0.302 Hom.: 2988

Bravo AF: 0.278

Asia WGS AF: 0.365 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.92
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs11176082; hg19: chr12-66580735;