12-28021884-C-T

Variant names:

• chr12-28021884-C-T
• rs7297051

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 0.218 in 152,148 control chromosomes in the GnomAD database, including 3,870 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 0.22 (3870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33222 AN: 152030 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.218 AC: 33240 AN: 152148 Hom.: 3870 Cov.: 32 AF XY: 0.218 AC XY: 16232 AN XY: 74384

African (AFR) AF: 0.142 AC: 5911 AN: 41512

American (AMR) AF: 0.291 AC: 4454 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1239 AN: 5182

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4814

European-Finnish (FIN) AF: 0.210 AC: 2218 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16513 AN: 68008

Other (OTH) AF: 0.226 AC: 477 AN: 2112

Alfa AF: 0.238 Hom.: 7849

Bravo AF: 0.224

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.80
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7297051; hg19: chr12-28174817;