rs10984096

chr9-118576812-A-Gchr9-118576812-A-T

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 0.202 in 151,558 control chromosomes in the GnomAD database, including 3,256 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 0.20 (3256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.202 AC: 30646 AN: 151440 Hom.: 3252 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.202 AC: 30682 AN: 151558 Hom.: 3256 Cov.: 32 AF XY: 0.202 AC XY: 14936 AN XY: 74084

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.190

Alfa AF: 0.174 Hom.: 1276

Bravo AF: 0.212

Asia WGS AF: 0.143 AC: 494 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
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: rs10984096; hg19: chr9-121339090;