rs13059218

Variant names:

• chr3-26869004-G-A
• rs13059218

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 0.163 in 151,990 control chromosomes in the GnomAD database, including 2,237 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 0.16 (2237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 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: 0.163 AC: 24821 AN: 151872 Hom.: 2232 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.163 AC: 24837 AN: 151990 Hom.: 2237 Cov.: 32 AF XY: 0.166 AC XY: 12364 AN XY: 74294

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.157

Alfa AF: 0.164 Hom.: 275

Bravo AF: 0.169

Asia WGS AF: 0.203 AC: 706 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13059218; hg19: chr3-26910495;