12-28021884-C-T

Variant names:

• chr12-28021884-C-T
• rs7297051

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.226

Alfa AF: 0.237 Hom.: 1465

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7297051; hg19: chr12-28174817;