chr11-100593522-C-G

Variant names:

• chr11-100593522-C-G
• rs12223916

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0815 in 152,220 control chromosomes in the GnomAD database, including 703 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 0.082 (703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12405 AN: 152102 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0815 AC: 12410 AN: 152220 Hom.: 703 Cov.: 32 AF XY: 0.0819 AC XY: 6098 AN XY: 74414

African (AFR) AF: 0.0188 AC: 780 AN: 41558

American (AMR) AF: 0.0775 AC: 1184 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1318 AN: 5162

South Asian (SAS) AF: 0.118 AC: 567 AN: 4812

European-Finnish (FIN) AF: 0.0876 AC: 928 AN: 10598

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6830 AN: 68018

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0846 Hom.: 77

Bravo AF: 0.0783

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs12223916; hg19: chr11-100464253;