16-54166302-G-A

Variant names:

• chr16-54166302-G-A
• rs12447727

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 0.0776 in 152,190 control chromosomes in the GnomAD database, including 552 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 0.078 (552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11792 AN: 152074 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0776 AC: 11811 AN: 152190 Hom.: 552 Cov.: 32 AF XY: 0.0791 AC XY: 5886 AN XY: 74404

African (AFR) AF: 0.0617 AC: 2562 AN: 41528

American (AMR) AF: 0.0911 AC: 1394 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 446 AN: 3472

East Asian (EAS) AF: 0.176 AC: 911 AN: 5166

South Asian (SAS) AF: 0.0996 AC: 479 AN: 4810

European-Finnish (FIN) AF: 0.0997 AC: 1058 AN: 10610

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0694 AC: 4720 AN: 67992

Other (OTH) AF: 0.0914 AC: 193 AN: 2112

Alfa AF: 0.0738 Hom.: 1405

Bravo AF: 0.0776

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.65
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs12447727; hg19: chr16-54200214;