16-86509796-A-G

Variant names:

• chr16-86509796-A-G
• rs1364224

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 0.684 in 151,566 control chromosomes in the GnomAD database, including 36,550 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 0.68 (36550 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103536 AN: 151458 Hom.: 36525 Cov.: 35

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.684 AC: 103605 AN: 151566 Hom.: 36550 Cov.: 35 AF XY: 0.688 AC XY: 50940 AN XY: 74048

African (AFR) AF: 0.491 AC: 20321 AN: 41350

American (AMR) AF: 0.801 AC: 12214 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2714 AN: 3466

East Asian (EAS) AF: 0.868 AC: 4407 AN: 5076

South Asian (SAS) AF: 0.674 AC: 3250 AN: 4822

European-Finnish (FIN) AF: 0.777 AC: 8183 AN: 10526

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.741 AC: 50220 AN: 67780

Other (OTH) AF: 0.713 AC: 1498 AN: 2102

Alfa AF: 0.700 Hom.: 8062

Bravo AF: 0.683

Asia WGS AF: 0.752 AC: 2601 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.38
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1364224; hg19: chr16-86543402;