rs12457166

Variant names:

• chr18-60236040-G-A
• rs12457166

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 0.123 in 151,844 control chromosomes in the GnomAD database, including 1,591 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 (1591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 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: 0.122 AC: 18586 AN: 151726 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0514

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.123 AC: 18622 AN: 151844 Hom.: 1591 Cov.: 32 AF XY: 0.125 AC XY: 9253 AN XY: 74218

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0514

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0725

Gnomad4 OTH AF: 0.0954

Alfa AF: 0.0791 Hom.: 815

Bravo AF: 0.119

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12457166; hg19: chr18-57903273;