rs9332102

Variant names:

• chr10-94938199-C-A
• rs9332102

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 0.0879 in 152,144 control chromosomes in the GnomAD database, including 741 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 0.088 (741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 10-94938199-C-A is Benign according to our data. Variant chr10-94938199-C-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0880 AC: 13371 AN: 152026 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0879 AC: 13366 AN: 152144 Hom.: 741 Cov.: 32 AF XY: 0.0866 AC XY: 6445 AN XY: 74380

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.0977

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.110

Alfa AF: 0.122 Hom.: 1109

Bravo AF: 0.0858

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.3
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332102; hg19: chr10-96697956;