rs12493123

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;