rs10886159

Variant names:

• chr10-117854099-T-C
• rs10886159

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.241 AC: 10003 AN: 41478

American (AMR) AF: 0.329 AC: 5021 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2792 AN: 5148

South Asian (SAS) AF: 0.140 AC: 677 AN: 4824

European-Finnish (FIN) AF: 0.219 AC: 2313 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16303 AN: 67970

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.257 Hom.: 7345

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10886159; hg19: chr10-119613610;