chr2-216104125-G-C

Variant names:

• chr2-216104125-G-C
• rs828918

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 0.888 in 152,320 control chromosomes in the GnomAD database, including 60,427 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 0.89 (60427 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135119 AN: 152202 Hom.: 60370 Cov.: 34

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.888 AC: 135234 AN: 152320 Hom.: 60427 Cov.: 34 AF XY: 0.886 AC XY: 65981 AN XY: 74476

African (AFR) AF: 0.969 AC: 40306 AN: 41576

American (AMR) AF: 0.895 AC: 13696 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4390 AN: 5188

South Asian (SAS) AF: 0.673 AC: 3244 AN: 4822

European-Finnish (FIN) AF: 0.921 AC: 9763 AN: 10606

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58099 AN: 68030

Other (OTH) AF: 0.862 AC: 1823 AN: 2116

Alfa AF: 0.868 Hom.: 2835

Bravo AF: 0.893

Asia WGS AF: 0.757 AC: 2631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.076
DANN	Benign	0.53
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs828918; hg19: chr2-216968848;