rs12686783

Variant names:

• chr9-99099485-C-T
• rs12686783

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.113 AC: 4697 AN: 41478

American (AMR) AF: 0.163 AC: 2485 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0861 AC: 299 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2115 AN: 5164

South Asian (SAS) AF: 0.166 AC: 798 AN: 4820

European-Finnish (FIN) AF: 0.143 AC: 1506 AN: 10562

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6686 AN: 67976

Other (OTH) AF: 0.122 AC: 259 AN: 2116

Alfa AF: 0.109 Hom.: 2792

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12686783; hg19: chr9-101861767;