rs9332093

Variant names:

• chr10-94936798-C-G
• rs9332093

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 0.0509 in 152,230 control chromosomes in the GnomAD database, including 249 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.051 (249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.107 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: 0.0509 AC: 7742 AN: 152112 Hom.: 250 Cov.: 32

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0509 AC: 7743 AN: 152230 Hom.: 249 Cov.: 32 AF XY: 0.0516 AC XY: 3839 AN XY: 74434

Gnomad4 AFR AF: 0.0175

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0584 Hom.: 32

Bravo AF: 0.0477

Asia WGS AF: 0.0780 AC: 272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332093; hg19: chr10-96696555;