rs16888589

Variant names:

• chr8-116623363-A-G
• rs16888589

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 0.093 in 152,084 control chromosomes in the GnomAD database, including 799 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 0.093 (799 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 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: 0.0930 AC: 14136 AN: 151966 Hom.: 798 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0705

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.0930 AC: 14138 AN: 152084 Hom.: 799 Cov.: 32 AF XY: 0.0942 AC XY: 7004 AN XY: 74374

African (AFR) AF: 0.134 AC: 5548 AN: 41444

American (AMR) AF: 0.0599 AC: 916 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3472

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0932 AC: 449 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1219 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5208 AN: 67992

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.0853 Hom.: 106

Bravo AF: 0.0898

Asia WGS AF: 0.0470 AC: 166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.55
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs16888589; hg19: chr8-117635602;