rs11230099

Positions:

• chr11-59913570-G-A

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 0.0855 in 152,152 control chromosomes in the GnomAD database, including 792 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 0.085 (792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 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: 0.0856 AC: 13007 AN: 152034 Hom.: 793 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00771

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0749

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

GnomAD4 genome AF: 0.0855 AC: 13008 AN: 152152 Hom.: 792 Cov.: 32 AF XY: 0.0890 AC XY: 6618 AN XY: 74386

Gnomad4 AFR AF: 0.0198

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.00773

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0741

Alfa AF: 0.116 Hom.: 548

Bravo AF: 0.0732

Asia WGS AF: 0.0770 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11230099; hg19: chr11-59681043;