16-28528527-C-T

Variant names:

• chr16-28528527-C-T
• rs4788084

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 0.36 in 151,918 control chromosomes in the GnomAD database, including 10,709 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 0.36 (10709 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 143 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 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: 0.360 AC: 54706 AN: 151800 Hom.: 10690 Cov.: 30

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.360 AC: 54761 AN: 151918 Hom.: 10709 Cov.: 30 AF XY: 0.361 AC XY: 26785 AN XY: 74240

African (AFR) AF: 0.247 AC: 10240 AN: 41470

American (AMR) AF: 0.417 AC: 6350 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1434 AN: 5154

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4824

European-Finnish (FIN) AF: 0.489 AC: 5143 AN: 10522

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28427 AN: 67946

Other (OTH) AF: 0.337 AC: 710 AN: 2104

Alfa AF: 0.390 Hom.: 39587

Bravo AF: 0.353

Asia WGS AF: 0.316 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.82
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs4788084; hg19: chr16-28539848;