rs10886159

Positions:

• chr10-117854099-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.256 in 152,068 control chromosomes in the GnomAD database, including 5,322 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 0.26 (5322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38873 AN: 151950 Hom.: 5308 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.256 AC: 38937 AN: 152068 Hom.: 5322 Cov.: 32 AF XY: 0.256 AC XY: 18993 AN XY: 74312

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.273

Alfa AF: 0.253 Hom.: 4784

Bravo AF: 0.272

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	11
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886159; hg19: chr10-119613610;