16-28086594-A-G

Variant names:

• chr16-28086594-A-G
• rs8051871

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0309

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.00735

Gnomad4 NFE AF: 0.00350

Gnomad4 OTH AF: 0.0828

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8051871; hg19: chr16-28097915;