rs9332100

Positions:

• chr10-94938063-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;