rs12282928

chr11-48310476-A-Gchr11-48310476-A-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 0.31 in 152,018 control chromosomes in the GnomAD database, including 8,094 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 0.31 (8094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47090 AN: 151900 Hom.: 8073 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.310 AC: 47157 AN: 152018 Hom.: 8094 Cov.: 32 AF XY: 0.311 AC XY: 23086 AN XY: 74318

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.321

Alfa AF: 0.265 Hom.: 5019

Bravo AF: 0.318

Asia WGS AF: 0.488 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12282928; hg19: chr11-48332028;