rs28463809

chr16-52549142-G-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 0.367 in 152,062 control chromosomes in the GnomAD database, including 11,274 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 0.37 (11274 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.367 AC: 55709 AN: 151942 Hom.: 11241 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.367 AC: 55808 AN: 152062 Hom.: 11274 Cov.: 32 AF XY: 0.369 AC XY: 27460 AN XY: 74320

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.362

Alfa AF: 0.299 Hom.: 3666

Bravo AF: 0.383

Asia WGS AF: 0.428 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.9
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28463809; hg19: chr16-52583054;