rs12486123

Variant names:

• chr3-30339345-A-G
• rs12486123

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 0.0874 in 152,126 control chromosomes in the GnomAD database, including 699 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 0.087 (699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.118 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: 0.0875 AC: 13299 AN: 152008 Hom.: 699 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0874 AC: 13303 AN: 152126 Hom.: 699 Cov.: 32 AF XY: 0.0867 AC XY: 6449 AN XY: 74368

African (AFR) AF: 0.0245 AC: 1017 AN: 41548

American (AMR) AF: 0.104 AC: 1593 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3470

East Asian (EAS) AF: 0.0431 AC: 222 AN: 5152

South Asian (SAS) AF: 0.0676 AC: 326 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1257 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8169 AN: 67960

Other (OTH) AF: 0.103 AC: 218 AN: 2110

Alfa AF: 0.108 Hom.: 219

Bravo AF: 0.0838

Asia WGS AF: 0.0630 AC: 219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.96
DANN	Benign	0.71
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12486123; hg19: chr3-30380837;