rs12477582

chr2-125506356-C-T

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 0.344 in 151,870 control chromosomes in the GnomAD database, including 10,662 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 0.34 (10662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.344 AC: 52145 AN: 151752 Hom.: 10639 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.344 AC: 52231 AN: 151870 Hom.: 10662 Cov.: 32 AF XY: 0.351 AC XY: 26034 AN XY: 74230

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.364

Alfa AF: 0.307 Hom.: 1315

Bravo AF: 0.368

Asia WGS AF: 0.689 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.2
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12477582; hg19: chr2-126263933;