rs11059856

Variant names:

• chr12-128725584-C-T
• rs11059856

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 0.533 in 151,996 control chromosomes in the GnomAD database, including 21,726 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 0.53 (21726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.533 AC: 80978 AN: 151878 Hom.: 21722 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.533 AC: 81024 AN: 151996 Hom.: 21726 Cov.: 32 AF XY: 0.533 AC XY: 39570 AN XY: 74282

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.518

Alfa AF: 0.554 Hom.: 14505

Bravo AF: 0.527

Asia WGS AF: 0.470 AC: 1633 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11059856; hg19: chr12-129210129;