rs10121793

Positions:

• chr9-82852892-A-G
• chr9-82852892-A-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 0.0805 in 152,156 control chromosomes in the GnomAD database, including 1,526 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 0.081 (1526 hom., cov: 32)
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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: 0.0804 AC: 12225 AN: 152038 Hom.: 1522 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.00999

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00243

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0805 AC: 12253 AN: 152156 Hom.: 1526 Cov.: 32 AF XY: 0.0781 AC XY: 5809 AN XY: 74412

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.00923

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.00974

Gnomad4 FIN AF: 0.00999

Gnomad4 NFE AF: 0.00243

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0174 Hom.: 50

Bravo AF: 0.0930

Asia WGS AF: 0.0460 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10121793; hg19: chr9-85467807;