rs11216943

chr11-118685689-G-A

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 0.204 in 151,996 control chromosomes in the GnomAD database, including 3,355 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 0.20 (3355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 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: 0.204 AC: 30926 AN: 151878 Hom.: 3352 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.204 AC: 30934 AN: 151996 Hom.: 3355 Cov.: 31 AF XY: 0.206 AC XY: 15313 AN XY: 74286

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.201

Alfa AF: 0.229 Hom.: 4587

Bravo AF: 0.191

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11216943; hg19: chr11-118556398;