rs12466120

Variant names:

• chr2-53360102-G-A
• rs12466120

Your query was ambiguous. Multiple possible variants found:

• chr2-53360102-G-A
• chr2-53360102-G-C

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 0.292 in 151,820 control chromosomes in the GnomAD database, including 6,722 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 0.29 (6722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

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 = 0.447 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: 0.292 AC: 44282 AN: 151702 Hom.: 6712 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.292 AC: 44322 AN: 151820 Hom.: 6722 Cov.: 32 AF XY: 0.296 AC XY: 21933 AN XY: 74192

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.275

Alfa AF: 0.231 Hom.: 3998

Bravo AF: 0.292

Asia WGS AF: 0.383 AC: 1332 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
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: rs12466120; hg19: chr2-53587240;