rs1566045

Variant names:

• chr16-50987892-T-C
• rs1566045

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 0.149 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
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.149 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

African (AFR) AF: 0.0492 AC: 2044 AN: 41526

American (AMR) AF: 0.205 AC: 3138 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3466

East Asian (EAS) AF: 0.136 AC: 701 AN: 5168

South Asian (SAS) AF: 0.0709 AC: 341 AN: 4808

European-Finnish (FIN) AF: 0.114 AC: 1212 AN: 10590

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13934 AN: 67968

Other (OTH) AF: 0.163 AC: 344 AN: 2106

Alfa AF: 0.189 Hom.: 8699

Bravo AF: 0.151

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.36
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1566045; hg19: chr16-51021803;