9-99099485-C-T

Position:

• chr9-99099485-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 0.125 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;