rs10811659

Variant names:

• chr9-22133717-T-C
• rs10811659

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 0.179 in 152,234 control chromosomes in the GnomAD database, including 2,826 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 0.18 (2826 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.179 AC: 27272 AN: 152116 Hom.: 2826 Cov.: 33

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.179 AC: 27278 AN: 152234 Hom.: 2826 Cov.: 33 AF XY: 0.178 AC XY: 13274 AN XY: 74420

Gnomad4 AFR AF: 0.0809

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.183

Alfa AF: 0.216 Hom.: 5610

Bravo AF: 0.166

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.2
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811659; hg19: chr9-22133716;