chr11-109076917-G-A

Variant names:

• chr11-109076917-G-A
• rs11212913

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 0.305 in 152,008 control chromosomes in the GnomAD database, including 7,932 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 0.31 (7932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46341 AN: 151890 Hom.: 7912 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.305 AC: 46406 AN: 152008 Hom.: 7932 Cov.: 32 AF XY: 0.308 AC XY: 22869 AN XY: 74302

African (AFR) AF: 0.458 AC: 18966 AN: 41436

American (AMR) AF: 0.327 AC: 4986 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1778 AN: 5156

South Asian (SAS) AF: 0.297 AC: 1435 AN: 4824

European-Finnish (FIN) AF: 0.266 AC: 2811 AN: 10570

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15026 AN: 67968

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.242 Hom.: 19172

Bravo AF: 0.319

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.30
DANN	Benign	0.74
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs11212913; hg19: chr11-108947644;