rs10089517

Variant names:

• chr8-59266162-C-A
• rs10089517

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 0.314 in 151,872 control chromosomes in the GnomAD database, including 8,182 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 0.31 (8182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 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: 0.314 AC: 47607 AN: 151754 Hom.: 8179 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.314 AC: 47636 AN: 151872 Hom.: 8182 Cov.: 32 AF XY: 0.311 AC XY: 23097 AN XY: 74224

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.359

Alfa AF: 0.354 Hom.: 9901

Bravo AF: 0.331

Asia WGS AF: 0.305 AC: 1053 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10089517; hg19: chr8-60178721;