16-28086594-A-G

Variant names:

• chr16-28086594-A-G
• rs8051871

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 0.0869 in 152,206 control chromosomes in the GnomAD database, including 1,324 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 0.087 (1324 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.0866 AC: 13165 AN: 152088 Hom.: 1307 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.00735

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00350

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0869 AC: 13229 AN: 152206 Hom.: 1324 Cov.: 33 AF XY: 0.0908 AC XY: 6756 AN XY: 74426

African (AFR) AF: 0.209 AC: 8688 AN: 41496

American (AMR) AF: 0.152 AC: 2325 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0309 AC: 107 AN: 3468

East Asian (EAS) AF: 0.176 AC: 907 AN: 5166

South Asian (SAS) AF: 0.145 AC: 702 AN: 4830

European-Finnish (FIN) AF: 0.00735 AC: 78 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00350 AC: 238 AN: 68012

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.0267 Hom.: 48

Bravo AF: 0.102

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.25
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs8051871; hg19: chr16-28097915;