rs2307803

chr3-109262182-TTG-Tchr3-109262182-TTG-TTGTG

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.252 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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.220

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2307803; hg19: chr3-108981029;