rs1566045

Variant names:

• chr16-50987892-T-C
• rs1566045

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 0.149 in 152,118 control chromosomes in the GnomAD database, including 2,128 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 0.15 (2128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 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: 0.149 AC: 22621 AN: 152000 Hom.: 2132 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.149 AC: 22601 AN: 152118 Hom.: 2128 Cov.: 32 AF XY: 0.145 AC XY: 10766 AN XY: 74360

Gnomad4 AFR AF: 0.0492

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0709

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.163

Alfa AF: 0.194 Hom.: 3503

Bravo AF: 0.151

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566045; hg19: chr16-51021803;