rs2307803

Variant names:

• chr3-109262182-TTG-T
• rs2307803

Your query was ambiguous. Multiple possible variants found:

• chr3-109262182-TTG-T
• chr3-109262182-TTG-TTGTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.252 in 152,016 control chromosomes in the GnomAD database, including 5,345 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5345 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.252 AC: 38267 AN: 151898 Hom.: 5326 Cov.: 24

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.252 AC: 38333 AN: 152016 Hom.: 5345 Cov.: 24 AF XY: 0.252 AC XY: 18714 AN XY: 74322

African (AFR) AF: 0.358 AC: 14828 AN: 41450

American (AMR) AF: 0.299 AC: 4567 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5172

South Asian (SAS) AF: 0.183 AC: 883 AN: 4826

European-Finnish (FIN) AF: 0.210 AC: 2219 AN: 10564

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13480 AN: 67960

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.238 Hom.: 546

Bravo AF: 0.262

Asia WGS AF: 0.187 AC: 650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs2307803; hg19: chr3-108981029;