rs2099106

Variant names:

• chr16-9286851-C-T
• rs2099106

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 0.218 in 151,964 control chromosomes in the GnomAD database, including 3,914 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 0.22 (3914 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 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: 0.218 AC: 33093 AN: 151846 Hom.: 3912 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.218 AC: 33116 AN: 151964 Hom.: 3914 Cov.: 31 AF XY: 0.219 AC XY: 16288 AN XY: 74260

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.208

Alfa AF: 0.223 Hom.: 674

Bravo AF: 0.208

Asia WGS AF: 0.238 AC: 828 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2099106; hg19: chr16-9380708;