rs283277

Variant names:

• chr20-54920285-C-A
• rs283277

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 0.174 in 152,214 control chromosomes in the GnomAD database, including 2,606 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 0.17 (2606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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: 0.174 AC: 26516 AN: 152096 Hom.: 2601 Cov.: 33

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.174 AC: 26523 AN: 152214 Hom.: 2606 Cov.: 33 AF XY: 0.171 AC XY: 12729 AN XY: 74412

Gnomad4 AFR AF: 0.0944

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0904

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.184

Alfa AF: 0.182 Hom.: 395

Bravo AF: 0.173

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283277; hg19: chr20-53536824;