16-26159619-G-A

Variant names:

• chr16-26159619-G-A
• rs9933429

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 0.241 in 152,040 control chromosomes in the GnomAD database, including 4,814 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 0.24 (4814 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36623 AN: 151920 Hom.: 4812 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.241 AC: 36642 AN: 152040 Hom.: 4814 Cov.: 32 AF XY: 0.246 AC XY: 18253 AN XY: 74322

African (AFR) AF: 0.141 AC: 5866 AN: 41468

American (AMR) AF: 0.300 AC: 4592 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1137 AN: 5186

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3267 AN: 10538

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18402 AN: 67972

Other (OTH) AF: 0.246 AC: 517 AN: 2104

Alfa AF: 0.256 Hom.: 21949

Bravo AF: 0.233

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9933429; hg19: chr16-26170940;