rs4788084

Positions:

• chr16-28528527-C-T

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 0.36 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.360 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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.337

Alfa AF: 0.392 Hom.: 16864

Bravo AF: 0.353

Asia WGS AF: 0.316 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4788084; hg19: chr16-28539848;