16-86402728-A-G

Position:

• chr16-86402728-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 0.918 in 152,054 control chromosomes in the GnomAD database, including 64,287 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 0.92 (64287 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139433 AN: 151936 Hom.: 64236 Cov.: 30

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.918 AC: 139540 AN: 152054 Hom.: 64287 Cov.: 30 AF XY: 0.914 AC XY: 67925 AN XY: 74296

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.907

Alfa AF: 0.933 Hom.: 37840

Bravo AF: 0.909

Asia WGS AF: 0.783 AC: 2722 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1687651; hg19: chr16-86436334;