chr12-666033-G-A

Variant names:

• chr12-666033-G-A
• rs11833579

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 0.255 in 151,392 control chromosomes in the GnomAD database, including 5,063 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 0.26 (5063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 57 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 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: 0.255 AC: 38618 AN: 151286 Hom.: 5061 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.255 AC: 38633 AN: 151392 Hom.: 5063 Cov.: 31 AF XY: 0.259 AC XY: 19117 AN XY: 73904

African (AFR) AF: 0.217 AC: 8958 AN: 41292

American (AMR) AF: 0.302 AC: 4591 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1852 AN: 5162

South Asian (SAS) AF: 0.360 AC: 1723 AN: 4788

European-Finnish (FIN) AF: 0.217 AC: 2237 AN: 10294

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17109 AN: 67888

Other (OTH) AF: 0.278 AC: 580 AN: 2090

Alfa AF: 0.242 Hom.: 3450

Bravo AF: 0.259

Asia WGS AF: 0.313 AC: 1085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.32
DANN	Benign	0.37
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11833579; hg19: chr12-775199;