rs9406815

chr9-24799886-C-Achr9-24799886-C-Gchr9-24799886-C-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 0.194 in 151,798 control chromosomes in the GnomAD database, including 3,816 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 0.19 (3816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.194 AC: 29449 AN: 151680 Hom.: 3806 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.194 AC: 29498 AN: 151798 Hom.: 3816 Cov.: 32 AF XY: 0.199 AC XY: 14750 AN XY: 74210

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.199

Alfa AF: 0.133 Hom.: 3457

Bravo AF: 0.204

Asia WGS AF: 0.411 AC: 1426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.062
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9406815; hg19: chr9-24799884;