chr11-2107800-A-G

Variant names:

• chr11-2107800-A-G
• rs7926624

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 0.0812 in 151,908 control chromosomes in the GnomAD database, including 612 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 0.081 (612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12296 AN: 151790 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0353

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0812 AC: 12328 AN: 151908 Hom.: 612 Cov.: 32 AF XY: 0.0796 AC XY: 5907 AN XY: 74232

African (AFR) AF: 0.138 AC: 5718 AN: 41418

American (AMR) AF: 0.0568 AC: 867 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3470

East Asian (EAS) AF: 0.000777 AC: 4 AN: 5146

South Asian (SAS) AF: 0.0355 AC: 169 AN: 4754

European-Finnish (FIN) AF: 0.0575 AC: 609 AN: 10590

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0665 AC: 4522 AN: 67958

Other (OTH) AF: 0.0855 AC: 180 AN: 2106

Alfa AF: 0.0579 Hom.: 131

Bravo AF: 0.0854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.44
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7926624; hg19: chr11-2129030;