16-86369512-C-T

Variant names:

• chr16-86369512-C-T
• rs9936833

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 0.639 in 151,988 control chromosomes in the GnomAD database, including 31,310 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 0.64 (31310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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: 0.639 AC: 96975 AN: 151870 Hom.: 31260 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.639 AC: 97083 AN: 151988 Hom.: 31310 Cov.: 32 AF XY: 0.642 AC XY: 47662 AN XY: 74280

African (AFR) AF: 0.661 AC: 27368 AN: 41406

American (AMR) AF: 0.586 AC: 8957 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2032 AN: 3468

East Asian (EAS) AF: 0.843 AC: 4366 AN: 5178

South Asian (SAS) AF: 0.564 AC: 2716 AN: 4818

European-Finnish (FIN) AF: 0.695 AC: 7331 AN: 10544

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42350 AN: 67990

Other (OTH) AF: 0.594 AC: 1250 AN: 2106

Alfa AF: 0.634 Hom.: 52913

Bravo AF: 0.633

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.8
DANN	Benign	0.60
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9936833; hg19: chr16-86403118;