rs6862233

Variant names:

• chr5-80105467-A-G
• rs6862233

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 0.332 in 151,736 control chromosomes in the GnomAD database, including 9,196 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 0.33 (9196 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.332 AC: 50293 AN: 151618 Hom.: 9186 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.332 AC: 50335 AN: 151736 Hom.: 9196 Cov.: 30 AF XY: 0.328 AC XY: 24296 AN XY: 74132

African (AFR) AF: 0.497 AC: 20520 AN: 41316

American (AMR) AF: 0.297 AC: 4527 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3466

East Asian (EAS) AF: 0.180 AC: 927 AN: 5138

South Asian (SAS) AF: 0.260 AC: 1248 AN: 4794

European-Finnish (FIN) AF: 0.230 AC: 2420 AN: 10536

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18483 AN: 67916

Other (OTH) AF: 0.322 AC: 677 AN: 2104

Alfa AF: 0.287 Hom.: 5059

Bravo AF: 0.343

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.53
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs6862233; hg19: chr5-79401290;