rs11166111

Variant names:

• chr1-98761221-G-A
• rs11166111

Your query was ambiguous. Multiple possible variants found:

• chr1-98761221-G-A
• chr1-98761221-G-C
• chr1-98761221-G-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 0.712 in 152,026 control chromosomes in the GnomAD database, including 39,991 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 0.71 (39991 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

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 (SAS) allele frequency at 95% confidence interval = 0.805 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: 0.712 AC: 108209 AN: 151906 Hom.: 39985 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.712 AC: 108268 AN: 152026 Hom.: 39991 Cov.: 33 AF XY: 0.714 AC XY: 53087 AN XY: 74314

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.715

Alfa AF: 0.755 Hom.: 5186

Bravo AF: 0.687

Asia WGS AF: 0.612 AC: 2126 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
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: rs11166111; hg19: chr1-99226777;