rs10811659

chr9-22133717-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;