3-162351221-G-A

Variant names:

• chr3-162351221-G-A
• rs12493123

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 0.417 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.406 AC: 16808 AN: 41400

American (AMR) AF: 0.362 AC: 5532 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3466

East Asian (EAS) AF: 0.116 AC: 598 AN: 5160

South Asian (SAS) AF: 0.398 AC: 1923 AN: 4826

European-Finnish (FIN) AF: 0.411 AC: 4338 AN: 10542

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31165 AN: 67914

Other (OTH) AF: 0.426 AC: 897 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.37
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12493123; hg19: chr3-162069009;