chr11-116793324-G-A

Variant names:

• chr11-116793324-G-A
• rs10750097

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 0.698 in 151,746 control chromosomes in the GnomAD database, including 37,825 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 0.70 (37825 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 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: 0.698 AC: 105786 AN: 151628 Hom.: 37803 Cov.: 30

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.698 AC: 105859 AN: 151746 Hom.: 37825 Cov.: 30 AF XY: 0.691 AC XY: 51245 AN XY: 74138

African (AFR) AF: 0.581 AC: 24002 AN: 41332

American (AMR) AF: 0.646 AC: 9832 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2609 AN: 3466

East Asian (EAS) AF: 0.583 AC: 2985 AN: 5122

South Asian (SAS) AF: 0.530 AC: 2551 AN: 4814

European-Finnish (FIN) AF: 0.729 AC: 7676 AN: 10524

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53806 AN: 67964

Other (OTH) AF: 0.700 AC: 1473 AN: 2104

Alfa AF: 0.755 Hom.: 66175

Bravo AF: 0.686

Asia WGS AF: 0.567 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10750097; hg19: chr11-116664040;