rs12457166

chr18-60236040-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;