rs11047921

Variant names:

• chr12-25255113-C-A
• rs11047921

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 0.0447 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0448 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

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0594 Hom.: 138

Bravo AF: 0.0359

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11047921; hg19: chr12-25408047;