rs12683493

Variant names:

• chr9-133279490-C-T
• rs12683493

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 0.158 in 152,146 control chromosomes in the GnomAD database, including 2,124 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 0.16 (2124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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 (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.158 AC: 24081 AN: 152028 Hom.: 2122 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.158 AC: 24089 AN: 152146 Hom.: 2124 Cov.: 32 AF XY: 0.155 AC XY: 11505 AN XY: 74358

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.178

Alfa AF: 0.172 Hom.: 229

Bravo AF: 0.156

Asia WGS AF: 0.100 AC: 348 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	2.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12683493; hg19: chr9-136155063;