rs12450119

Positions:

• chr17-2517640-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 0.185 in 151,868 control chromosomes in the GnomAD database, including 2,675 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 0.18 (2675 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 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: 0.185 AC: 28043 AN: 151750 Hom.: 2669 Cov.: 30

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.185 AC: 28085 AN: 151868 Hom.: 2675 Cov.: 30 AF XY: 0.187 AC XY: 13889 AN XY: 74256

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.179

Alfa AF: 0.162 Hom.: 4315

Bravo AF: 0.188

Asia WGS AF: 0.306 AC: 1064 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	1.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12450119; hg19: chr17-2420934;