rs10501093

Variant names:

• chr11-27968572-G-A
• rs10501093

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 0.0904 in 151,998 control chromosomes in the GnomAD database, including 894 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 0.090 (894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.0904 AC: 13735 AN: 151880 Hom.: 894 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0925

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

GnomAD4 genome AF: 0.0904 AC: 13736 AN: 151998 Hom.: 894 Cov.: 32 AF XY: 0.0888 AC XY: 6596 AN XY: 74278

African (AFR) AF: 0.0230 AC: 956 AN: 41492

American (AMR) AF: 0.0695 AC: 1060 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3462

East Asian (EAS) AF: 0.165 AC: 851 AN: 5160

South Asian (SAS) AF: 0.195 AC: 938 AN: 4812

European-Finnish (FIN) AF: 0.0505 AC: 535 AN: 10588

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8498 AN: 67928

Other (OTH) AF: 0.0930 AC: 196 AN: 2108

Alfa AF: 0.114 Hom.: 1826

Bravo AF: 0.0860

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs10501093; hg19: chr11-27990119;