11-116834384-G-T

Variant names:

• chr11-116834384-G-T
• rs11216153

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.162 in 152,090 control chromosomes in the GnomAD database, including 2,140 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 0.16 (2140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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: 0.162 AC: 24656 AN: 151978 Hom.: 2130 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.162 AC: 24703 AN: 152090 Hom.: 2140 Cov.: 32 AF XY: 0.166 AC XY: 12368 AN XY: 74348

African (AFR) AF: 0.107 AC: 4459 AN: 41484

American (AMR) AF: 0.209 AC: 3200 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1430 AN: 5150

South Asian (SAS) AF: 0.203 AC: 977 AN: 4822

European-Finnish (FIN) AF: 0.223 AC: 2358 AN: 10574

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11212 AN: 67984

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.117 Hom.: 213

Bravo AF: 0.162

Asia WGS AF: 0.228 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs11216153; hg19: chr11-116705100;