rs3093230

Variant names:

• chr13-113103654-G-A
• rs3093230

Your query was ambiguous. Multiple possible variants found:

• chr13-113103654-G-A
• chr13-113103654-G-C

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 0.195 in 152,100 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: 1.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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: 0.195 AC: 29591 AN: 151982 Hom.: 3639 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.195 AC: 29600 AN: 152100 Hom.: 3646 Cov.: 32 AF XY: 0.200 AC XY: 14841 AN XY: 74346

African (AFR) AF: 0.0633 AC: 2627 AN: 41532

American (AMR) AF: 0.253 AC: 3861 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2309 AN: 5146

South Asian (SAS) AF: 0.154 AC: 741 AN: 4808

European-Finnish (FIN) AF: 0.322 AC: 3411 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15741 AN: 67952

Other (OTH) AF: 0.174 AC: 369 AN: 2116

Alfa AF: 0.202 Hom.: 601

Bravo AF: 0.190

Asia WGS AF: 0.288 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs3093230; hg19: chr13-113757968; COSMIC: COSV60645537;