chr11-11206827-C-G

Variant names:

• chr11-11206827-C-G
• rs2722769

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 0.309 in 152,172 control chromosomes in the GnomAD database, including 8,936 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 (8936 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.309 AC: 47049 AN: 152054 Hom.: 8935 Cov.: 33

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.309 AC: 47036 AN: 152172 Hom.: 8936 Cov.: 33 AF XY: 0.307 AC XY: 22825 AN XY: 74372

African (AFR) AF: 0.0842 AC: 3500 AN: 41554

American (AMR) AF: 0.310 AC: 4741 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2674 AN: 5164

South Asian (SAS) AF: 0.315 AC: 1520 AN: 4818

European-Finnish (FIN) AF: 0.396 AC: 4182 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.415 AC: 28239 AN: 67986

Other (OTH) AF: 0.296 AC: 625 AN: 2110

Alfa AF: 0.376 Hom.: 6097

Bravo AF: 0.292

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.66
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs2722769; hg19: chr11-11228374;