rs13081389

chr3-12248301-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 0.0484 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.0279

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.0855

Gnomad4 NFE AF: 0.0628

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0569 Hom.: 310

Bravo AF: 0.0418

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	11
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13081389; hg19: chr3-12289800;