rs10966811

chr9-25233486-G-Achr9-25233486-G-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 0.329 in 151,996 control chromosomes in the GnomAD database, including 9,865 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 0.33 (9865 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.329 AC: 49972 AN: 151878 Hom.: 9879 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.329 AC: 49948 AN: 151996 Hom.: 9865 Cov.: 33 AF XY: 0.328 AC XY: 24363 AN XY: 74272

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.343

Alfa AF: 0.404 Hom.: 16049

Bravo AF: 0.322

Asia WGS AF: 0.354 AC: 1229 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.45
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10966811; hg19: chr9-25233484; COSMIC: COSV60344305;