chr12-84547650-A-G

Variant names:

• chr12-84547650-A-G
• rs2125716

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 0.81 in 152,084 control chromosomes in the GnomAD database, including 50,326 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 0.81 (50326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.811 AC: 123173 AN: 151966 Hom.: 50289 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.810 AC: 123261 AN: 152084 Hom.: 50326 Cov.: 32 AF XY: 0.812 AC XY: 60330 AN XY: 74334

African (AFR) AF: 0.889 AC: 36891 AN: 41502

American (AMR) AF: 0.738 AC: 11264 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2195 AN: 3466

East Asian (EAS) AF: 0.932 AC: 4829 AN: 5180

South Asian (SAS) AF: 0.812 AC: 3910 AN: 4816

European-Finnish (FIN) AF: 0.868 AC: 9193 AN: 10590

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52547 AN: 67950

Other (OTH) AF: 0.769 AC: 1623 AN: 2110

Alfa AF: 0.766 Hom.: 73077

Bravo AF: 0.804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2125716; hg19: chr12-84941429;