rs12223916

Variant names:

• chr11-100593522-C-G
• rs12223916

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0816 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

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0946

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12223916; hg19: chr11-100464253;