rs10886051

chr10-117234968-C-Achr10-117234968-C-T

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 0.187 in 152,168 control chromosomes in the GnomAD database, including 3,541 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 0.19 (3541 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28409 AN: 152050 Hom.: 3533 Cov.: 34

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.187 AC: 28426 AN: 152168 Hom.: 3541 Cov.: 34 AF XY: 0.187 AC XY: 13888 AN XY: 74396

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.188

Alfa AF: 0.223 Hom.: 7253

Bravo AF: 0.180

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886051; hg19: chr10-118994479;