rs11193561

Variant names:

• chr10-107614626-C-T
• rs11193561

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 0.227 in 151,972 control chromosomes in the GnomAD database, including 3,932 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 0.23 (3932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 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: 0.227 AC: 34522 AN: 151854 Hom.: 3933 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.227 AC: 34527 AN: 151972 Hom.: 3932 Cov.: 32 AF XY: 0.227 AC XY: 16825 AN XY: 74272

African (AFR) AF: 0.197 AC: 8176 AN: 41484

American (AMR) AF: 0.269 AC: 4095 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5158

South Asian (SAS) AF: 0.182 AC: 877 AN: 4822

European-Finnish (FIN) AF: 0.239 AC: 2534 AN: 10584

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16204 AN: 67896

Other (OTH) AF: 0.250 AC: 528 AN: 2108

Alfa AF: 0.239 Hom.: 12927

Bravo AF: 0.233

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.44
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs11193561; hg19: chr10-109374384;