rs9332092

Variant names:

• chr10-94936772-T-C
• rs9332092

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 0.0494 in 152,240 control chromosomes in the GnomAD database, including 245 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 0.049 (245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 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: 0.0495 AC: 7534 AN: 152122 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0494 AC: 7527 AN: 152240 Hom.: 245 Cov.: 32 AF XY: 0.0500 AC XY: 3722 AN XY: 74442

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0491

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.0315

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0643 Hom.: 297

Bravo AF: 0.0462

Asia WGS AF: 0.0760 AC: 266 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332092; hg19: chr10-96696529;