rs16988102

Variant names:

• chr2-20856402-C-G
• rs16988102

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 0.107 in 152,258 control chromosomes in the GnomAD database, including 1,047 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 0.11 (1047 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16270 AN: 152140 Hom.: 1045 Cov.: 33

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.107 AC: 16277 AN: 152258 Hom.: 1047 Cov.: 33 AF XY: 0.108 AC XY: 8034 AN XY: 74444

African (AFR) AF: 0.0349 AC: 1449 AN: 41572

American (AMR) AF: 0.101 AC: 1549 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3472

East Asian (EAS) AF: 0.137 AC: 711 AN: 5180

South Asian (SAS) AF: 0.127 AC: 613 AN: 4818

European-Finnish (FIN) AF: 0.165 AC: 1752 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9505 AN: 68012

Other (OTH) AF: 0.0960 AC: 203 AN: 2114

Alfa AF: 0.119 Hom.: 160

Bravo AF: 0.0998

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs16988102; hg19: chr2-21056162;