rs11218108

Variant names:

• chr11-121008207-T-C
• rs11218108

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 0.471 in 152,016 control chromosomes in the GnomAD database, including 17,293 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 0.47 (17293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 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: 0.471 AC: 71556 AN: 151898 Hom.: 17287 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.471 AC: 71604 AN: 152016 Hom.: 17293 Cov.: 32 AF XY: 0.473 AC XY: 35165 AN XY: 74304

African (AFR) AF: 0.380 AC: 15750 AN: 41454

American (AMR) AF: 0.540 AC: 8253 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5154

South Asian (SAS) AF: 0.414 AC: 1995 AN: 4816

European-Finnish (FIN) AF: 0.547 AC: 5779 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34530 AN: 67964

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.476 Hom.: 3346

Bravo AF: 0.467

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs11218108; hg19: chr11-120878916;