10-117556647-C-T

Variant names:

• chr10-117556647-C-T
• rs855766

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 0.388 in 151,994 control chromosomes in the GnomAD database, including 11,928 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 0.39 (11928 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.5 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: 0.388 AC: 58896 AN: 151876 Hom.: 11924 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.388 AC: 58937 AN: 151994 Hom.: 11928 Cov.: 31 AF XY: 0.394 AC XY: 29224 AN XY: 74264

African (AFR) AF: 0.481 AC: 19945 AN: 41424

American (AMR) AF: 0.370 AC: 5659 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1278 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2198 AN: 5172

South Asian (SAS) AF: 0.517 AC: 2487 AN: 4812

European-Finnish (FIN) AF: 0.392 AC: 4133 AN: 10550

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22148 AN: 67962

Other (OTH) AF: 0.338 AC: 713 AN: 2110

Alfa AF: 0.373 Hom.: 1779

Bravo AF: 0.382

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.59
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs855766; hg19: chr10-119316158;