rs11059856

chr12-128725584-C-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 0.533 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;