rs12353214

Variant names:

• chr9-122399591-C-T
• rs12353214

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 0.0993 in 152,112 control chromosomes in the GnomAD database, including 1,246 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 0.099 (1246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.0994 AC: 15101 AN: 151994 Hom.: 1246 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0725

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0993 AC: 15100 AN: 152112 Hom.: 1246 Cov.: 32 AF XY: 0.107 AC XY: 7949 AN XY: 74342

Gnomad4 AFR AF: 0.0230

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.0725

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.0962 Hom.: 155

Bravo AF: 0.0875

Asia WGS AF: 0.252 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12353214; hg19: chr9-125161870;