11-11206827-C-G

Variant names:

• chr11-11206827-C-G
• rs2722769

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 0.309 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.309 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

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.296

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2722769; hg19: chr11-11228374;