rs11059856

Variant names:

• chr12-128725584-C-T
• rs11059856

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 0.533 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.480 AC: 19886 AN: 41456

American (AMR) AF: 0.517 AC: 7904 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2043 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2459 AN: 5172

South Asian (SAS) AF: 0.531 AC: 2542 AN: 4786

European-Finnish (FIN) AF: 0.593 AC: 6267 AN: 10560

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38070 AN: 67962

Other (OTH) AF: 0.518 AC: 1091 AN: 2106

Alfa AF: 0.546 Hom.: 20008

Bravo AF: 0.527

Asia WGS AF: 0.470 AC: 1633 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs11059856; hg19: chr12-129210129;