rs11166111

chr1-98761221-G-Achr1-98761221-G-Cchr1-98761221-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;