rs12486123

Positions:

• chr3-30339345-A-G

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 0.0874 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

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 (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.103

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12486123; hg19: chr3-30380837;