rs10809826

chr9-12682663-C-Gchr9-12682663-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 0.427 in 151,930 control chromosomes in the GnomAD database, including 17,598 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 0.43 (17598 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494

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 (NFE) allele frequency at 95% confidence interval = 0.615 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: 0.427 AC: 64855 AN: 151812 Hom.: 17599 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.427 AC: 64866 AN: 151930 Hom.: 17598 Cov.: 31 AF XY: 0.420 AC XY: 31183 AN XY: 74248

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.0167

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.428

Alfa AF: 0.399 Hom.: 1385

Bravo AF: 0.392

Asia WGS AF: 0.132 AC: 460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10809826; hg19: chr9-12682663;