16-86402728-A-G

Variant names:

• chr16-86402728-A-G
• rs1687651

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 0.918 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.945 AC: 39217 AN: 41484

American (AMR) AF: 0.838 AC: 12798 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3250 AN: 3472

East Asian (EAS) AF: 0.676 AC: 3470 AN: 5136

South Asian (SAS) AF: 0.835 AC: 4009 AN: 4804

European-Finnish (FIN) AF: 0.955 AC: 10100 AN: 10576

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63660 AN: 67984

Other (OTH) AF: 0.907 AC: 1917 AN: 2114

Alfa AF: 0.930 Hom.: 52794

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
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs1687651; hg19: chr16-86436334;