rs3093233

Variant names:

• chr13-113103816-A-G
• rs3093233

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 0.19 in 152,030 control chromosomes in the GnomAD database, including 3,646 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 0.19 (3646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28833 AN: 151912 Hom.: 3637 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.190 AC: 28879 AN: 152030 Hom.: 3646 Cov.: 32 AF XY: 0.189 AC XY: 14025 AN XY: 74316

African (AFR) AF: 0.354 AC: 14679 AN: 41448

American (AMR) AF: 0.150 AC: 2290 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3472

East Asian (EAS) AF: 0.0397 AC: 205 AN: 5160

South Asian (SAS) AF: 0.272 AC: 1304 AN: 4802

European-Finnish (FIN) AF: 0.0763 AC: 808 AN: 10594

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8294 AN: 67944

Other (OTH) AF: 0.190 AC: 402 AN: 2114

Alfa AF: 0.153 Hom.: 2123

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs3093233; hg19: chr13-113758130;