16-20110968-A-G

Variant names:

• chr16-20110968-A-G
• rs2608200

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 0.79 in 152,074 control chromosomes in the GnomAD database, including 47,722 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 0.79 (47722 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.790 AC: 120006 AN: 151954 Hom.: 47669 Cov.: 30

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.790 AC: 120117 AN: 152074 Hom.: 47722 Cov.: 30 AF XY: 0.788 AC XY: 58576 AN XY: 74338

African (AFR) AF: 0.885 AC: 36751 AN: 41508

American (AMR) AF: 0.765 AC: 11686 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2934 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3777 AN: 5158

South Asian (SAS) AF: 0.791 AC: 3815 AN: 4824

European-Finnish (FIN) AF: 0.736 AC: 7770 AN: 10562

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50902 AN: 67958

Other (OTH) AF: 0.797 AC: 1681 AN: 2110

Alfa AF: 0.796 Hom.: 28326

Bravo AF: 0.795

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.38
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2608200; hg19: chr16-20122290;