11-48310476-A-G

Variant names:

• chr11-48310476-A-G
• rs12282928

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 0.31 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.441 AC: 18258 AN: 41430

American (AMR) AF: 0.263 AC: 4019 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2185 AN: 5170

South Asian (SAS) AF: 0.455 AC: 2194 AN: 4818

European-Finnish (FIN) AF: 0.189 AC: 1996 AN: 10578

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16520 AN: 67974

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.267 Hom.: 6153

Bravo AF: 0.318

Asia WGS AF: 0.488 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.78
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12282928; hg19: chr11-48332028;