rs793045

chr20-54345778-G-C

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 0.106 in 151,754 control chromosomes in the GnomAD database, including 2,679 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 0.11 (2679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.106 AC: 16098 AN: 151636 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.0227

Gnomad FIN AF: 0.00757

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00432

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.106 AC: 16119 AN: 151754 Hom.: 2679 Cov.: 32 AF XY: 0.103 AC XY: 7649 AN XY: 74188

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.0221

Gnomad4 FIN AF: 0.00757

Gnomad4 NFE AF: 0.00432

Gnomad4 OTH AF: 0.0763

Alfa AF: 0.0745 Hom.: 220

Bravo AF: 0.121

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.26
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs793045; hg19: chr20-52962317;