16-86509796-A-G

Position:

• chr16-86509796-A-G

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 0.684 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.713

Alfa AF: 0.708 Hom.: 7051

Bravo AF: 0.683

Asia WGS AF: 0.752 AC: 2601 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364224; hg19: chr16-86543402;