rs10759199

Variant names:

• chr9-106783782-G-C
• rs10759199

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 0.865 in 152,010 control chromosomes in the GnomAD database, including 57,103 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 0.86 (57103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.865 AC: 131356 AN: 151892 Hom.: 57052 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.865 AC: 131461 AN: 152010 Hom.: 57103 Cov.: 32 AF XY: 0.868 AC XY: 64477 AN XY: 74302

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.867

Alfa AF: 0.884 Hom.: 7418

Bravo AF: 0.856

Asia WGS AF: 0.910 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10759199; hg19: chr9-109546063;