12-66092543-A-G

Variant names:

• chr12-66092543-A-G
• rs2870783

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 0.445 in 150,060 control chromosomes in the GnomAD database, including 15,550 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 0.44 (15550 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.445 AC: 66665 AN: 149956 Hom.: 15525 Cov.: 28

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.445 AC: 66734 AN: 150060 Hom.: 15550 Cov.: 28 AF XY: 0.450 AC XY: 32904 AN XY: 73090

African (AFR) AF: 0.434 AC: 17717 AN: 40794

American (AMR) AF: 0.338 AC: 5128 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1740 AN: 3452

East Asian (EAS) AF: 0.860 AC: 4398 AN: 5112

South Asian (SAS) AF: 0.570 AC: 2706 AN: 4746

European-Finnish (FIN) AF: 0.473 AC: 4705 AN: 9952

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.430 AC: 29055 AN: 67586

Other (OTH) AF: 0.396 AC: 822 AN: 2076

Alfa AF: 0.413 Hom.: 1615

Bravo AF: 0.435

Asia WGS AF: 0.663 AC: 2299 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2870783; hg19: chr12-66486323;