10-117556647-C-T

Variant names:

• chr10-117556647-C-T
• rs855766

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.338

Alfa AF: 0.368 Hom.: 1657

Bravo AF: 0.382

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs855766; hg19: chr10-119316158;