rs16915515

Variant names:

• chr8-93070599-A-G
• rs16915515

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 0.0899 in 152,084 control chromosomes in the GnomAD database, including 885 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 0.090 (885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13653 AN: 151966 Hom.: 884 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0899 AC: 13665 AN: 152084 Hom.: 885 Cov.: 32 AF XY: 0.0931 AC XY: 6921 AN XY: 74342

Gnomad4 AFR AF: 0.0379

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0890 Hom.: 151

Bravo AF: 0.0945

Asia WGS AF: 0.248 AC: 859 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16915515; hg19: chr8-94082827;