rs13081389

Variant names:

• chr3-12248301-A-G
• rs13081389

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 0.0484 in 152,184 control chromosomes in the GnomAD database, including 204 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 0.048 (204 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 51 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 7368 AN: 152066 Hom.: 202 Cov.: 31

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0484 AC: 7372 AN: 152184 Hom.: 204 Cov.: 31 AF XY: 0.0496 AC XY: 3691 AN XY: 74388

African (AFR) AF: 0.0254 AC: 1056 AN: 41508

American (AMR) AF: 0.0279 AC: 426 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3468

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5188

South Asian (SAS) AF: 0.0752 AC: 362 AN: 4816

European-Finnish (FIN) AF: 0.0855 AC: 904 AN: 10578

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0628 AC: 4273 AN: 68014

Other (OTH) AF: 0.0270 AC: 57 AN: 2114

Alfa AF: 0.0540 Hom.: 501

Bravo AF: 0.0418

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs13081389; hg19: chr3-12289800;