rs9332098

Variant names:

• chr10-94937702-G-A
• rs9332098

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0496 in 152,260 control chromosomes in the GnomAD database, including 246 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.050 (246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 0.0497 AC: 7561 AN: 152142 Hom.: 247 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0496 AC: 7555 AN: 152260 Hom.: 246 Cov.: 32 AF XY: 0.0503 AC XY: 3741 AN XY: 74440

African (AFR) AF: 0.0131 AC: 545 AN: 41570

American (AMR) AF: 0.0492 AC: 753 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5182

South Asian (SAS) AF: 0.115 AC: 552 AN: 4818

European-Finnish (FIN) AF: 0.0562 AC: 596 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0662 AC: 4504 AN: 68002

Other (OTH) AF: 0.0522 AC: 110 AN: 2108

Alfa AF: 0.0555 Hom.: 132

Bravo AF: 0.0465

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.72
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs9332098; hg19: chr10-96697459;