20-5298223-A-G

Variant names:

• chr20-5298223-A-G
• rs10485484

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 0.329 in 152,108 control chromosomes in the GnomAD database, including 8,607 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 0.33 (8607 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50026 AN: 151990 Hom.: 8596 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.329 AC: 50051 AN: 152108 Hom.: 8607 Cov.: 31 AF XY: 0.328 AC XY: 24406 AN XY: 74358

African (AFR) AF: 0.225 AC: 9349 AN: 41502

American (AMR) AF: 0.314 AC: 4792 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1171 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2090 AN: 5158

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3325 AN: 10596

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26125 AN: 67972

Other (OTH) AF: 0.331 AC: 699 AN: 2112

Alfa AF: 0.351 Hom.: 4966

Bravo AF: 0.323

Asia WGS AF: 0.348 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10485484; hg19: chr20-5278869;