chr12-28021884-C-T

Position:

• chr12-28021884-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;