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. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.344 AC: 14256 AN: 41446

American (AMR) AF: 0.293 AC: 4475 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3464

East Asian (EAS) AF: 0.462 AC: 2379 AN: 5146

South Asian (SAS) AF: 0.318 AC: 1530 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3327 AN: 10550

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16698 AN: 67836

Other (OTH) AF: 0.275 AC: 578 AN: 2104

Alfa AF: 0.240 Hom.: 5708

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
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs12466120; hg19: chr2-53587240;