6-33107858-A-G

Variant names:

• chr6-33107858-A-G
• rs3117230

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 0.273 in 151,828 control chromosomes in the GnomAD database, including 6,218 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 0.27 (6218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41416 AN: 151710 Hom.: 6211 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.273 AC: 41441 AN: 151828 Hom.: 6218 Cov.: 32 AF XY: 0.269 AC XY: 19930 AN XY: 74184

African (AFR) AF: 0.411 AC: 17030 AN: 41400

American (AMR) AF: 0.220 AC: 3348 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3466

East Asian (EAS) AF: 0.151 AC: 783 AN: 5172

South Asian (SAS) AF: 0.259 AC: 1243 AN: 4800

European-Finnish (FIN) AF: 0.218 AC: 2292 AN: 10514

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15604 AN: 67922

Other (OTH) AF: 0.266 AC: 561 AN: 2108

Alfa AF: 0.233 Hom.: 16109

Bravo AF: 0.274

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.80
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3117230; hg19: chr6-33075635;