chr9-99099485-C-T

Variant names:

• chr9-99099485-C-T
• rs12686783

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 0.125 in 152,074 control chromosomes in the GnomAD database, including 1,483 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 0.12 (1483 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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 (EAS) allele frequency at 95% confidence interval = 0.395 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: 0.125 AC: 18932 AN: 151956 Hom.: 1486 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.125 AC: 18948 AN: 152074 Hom.: 1483 Cov.: 32 AF XY: 0.130 AC XY: 9688 AN XY: 74342

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0861

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.122

Alfa AF: 0.105 Hom.: 1031

Bravo AF: 0.127

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12686783; hg19: chr9-101861767;