rs12493123

Variant names:

• chr3-162351221-G-A
• rs12493123

Your query was ambiguous. Multiple possible variants found:

• chr3-162351221-G-A
• chr3-162351221-G-C

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 0.417 in 151,880 control chromosomes in the GnomAD database, including 13,586 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 0.42 (13586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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: 0.418 AC: 63367 AN: 151762 Hom.: 13575 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.417 AC: 63408 AN: 151880 Hom.: 13586 Cov.: 32 AF XY: 0.411 AC XY: 30534 AN XY: 74234

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.426

Alfa AF: 0.289 Hom.: 678

Bravo AF: 0.412

Asia WGS AF: 0.264 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12493123; hg19: chr3-162069009;