rs12477582

Variant names:

• chr2-125506356-C-T
• rs12477582

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 0.344 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.437 AC: 18091 AN: 41392

American (AMR) AF: 0.451 AC: 6872 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1285 AN: 3464

East Asian (EAS) AF: 0.870 AC: 4482 AN: 5152

South Asian (SAS) AF: 0.512 AC: 2466 AN: 4820

European-Finnish (FIN) AF: 0.189 AC: 2003 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15863 AN: 67910

Other (OTH) AF: 0.364 AC: 766 AN: 2104

Alfa AF: 0.310 Hom.: 1383

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12477582; hg19: chr2-126263933;