rs10089517

Positions:

• chr8-59266162-C-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;