chr12-28591708-C-T

Variant names:

• chr12-28591708-C-T
• rs10843215

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 0.875 in 152,112 control chromosomes in the GnomAD database, including 58,663 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 0.87 (58663 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 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: 0.875 AC: 132947 AN: 151994 Hom.: 58614 Cov.: 30

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.875 AC: 133054 AN: 152112 Hom.: 58663 Cov.: 30 AF XY: 0.873 AC XY: 64903 AN XY: 74360

African (AFR) AF: 0.854 AC: 35436 AN: 41492

American (AMR) AF: 0.801 AC: 12246 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2846 AN: 5128

South Asian (SAS) AF: 0.871 AC: 4202 AN: 4822

European-Finnish (FIN) AF: 0.919 AC: 9733 AN: 10588

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62471 AN: 68006

Other (OTH) AF: 0.887 AC: 1876 AN: 2114

Alfa AF: 0.897 Hom.: 180782

Bravo AF: 0.858

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.53
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10843215; hg19: chr12-28744641;