rs16888589

Positions:

• chr8-116623363-A-G

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 0.093 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0766

Gnomad4 OTH AF: 0.0890

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16888589; hg19: chr8-117635602;