rs2099106

Variant names:

• chr16-9286851-C-T
• rs2099106

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 0.218 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.135 AC: 5614 AN: 41472

American (AMR) AF: 0.200 AC: 3054 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1281 AN: 5168

South Asian (SAS) AF: 0.217 AC: 1044 AN: 4812

European-Finnish (FIN) AF: 0.300 AC: 3154 AN: 10508

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17318 AN: 67952

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.220 Hom.: 685

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2099106; hg19: chr16-9380708;