chr20-54920285-C-A

Position:

• chr20-54920285-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;