chr11-59913570-G-A

Variant names:

• chr11-59913570-G-A
• rs11230099

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 0.0855 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0198 AC: 823 AN: 41536

American (AMR) AF: 0.0575 AC: 879 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.00773 AC: 40 AN: 5174

South Asian (SAS) AF: 0.170 AC: 816 AN: 4810

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10592

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8137 AN: 67962

Other (OTH) AF: 0.0741 AC: 156 AN: 2106

Alfa AF: 0.115 Hom.: 593

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11230099; hg19: chr11-59681043;