rs12466120

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.53360102G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;