rs11066587

Variant names:

• chr12-113541851-C-G
• rs11066587

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 0.135 in 152,170 control chromosomes in the GnomAD database, including 2,132 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 0.14 (2132 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

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 (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.135 AC: 20572 AN: 152052 Hom.: 2116 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0552

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.135 AC: 20616 AN: 152170 Hom.: 2132 Cov.: 33 AF XY: 0.139 AC XY: 10317 AN XY: 74394

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0475

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0552

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0735 Hom.: 374

Bravo AF: 0.137

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11066587; hg19: chr12-113979656;