20-5298223-A-G

Variant names:

• chr20-5298223-A-G
• rs10485484

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.329 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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.331

Alfa AF: 0.349 Hom.: 4367

Bravo AF: 0.323

Asia WGS AF: 0.348 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485484; hg19: chr20-5278869;