rs11047921

Variant names:

• chr12-25255113-C-A
• rs11047921

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 0.0447 in 152,244 control chromosomes in the GnomAD database, including 260 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 0.045 (260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0625 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6808 AN: 152126 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0447 AC: 6809 AN: 152244 Hom.: 260 Cov.: 32 AF XY: 0.0457 AC XY: 3405 AN XY: 74430

African (AFR) AF: 0.0108 AC: 448 AN: 41556

American (AMR) AF: 0.0212 AC: 324 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0497 AC: 240 AN: 4826

European-Finnish (FIN) AF: 0.115 AC: 1218 AN: 10580

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4361 AN: 68014

Other (OTH) AF: 0.0336 AC: 71 AN: 2116

Alfa AF: 0.0588 Hom.: 155

Bravo AF: 0.0359

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.78
DANN	Benign	0.34
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11047921; hg19: chr12-25408047;