rs9332100

Variant names:

• chr10-94938063-G-T
• rs9332100

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.0899 in 152,006 control chromosomes in the GnomAD database, including 780 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 0.090 (780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 10-94938063-G-T is Benign according to our data. Variant chr10-94938063-G-T is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.0900 AC: 13666 AN: 151888 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0899 AC: 13661 AN: 152006 Hom.: 780 Cov.: 32 AF XY: 0.0894 AC XY: 6638 AN XY: 74276

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0982

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0395

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.110

Alfa AF: 0.105 Hom.: 138

Bravo AF: 0.0865

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332100; hg19: chr10-96697820;