rs9406815

Variant names:

• chr9-24799886-C-A
• rs9406815

Your query was ambiguous. Multiple possible variants found:

• chr9-24799886-C-A
• chr9-24799886-C-G
• chr9-24799886-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;