rs793046

Positions:

• chr20-54345649-C-T

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 0.105 in 151,976 control chromosomes in the GnomAD database, including 2,666 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 0.10 (2666 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54345649C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15883 AN: 151858 Hom.: 2663 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.0225

Gnomad FIN AF: 0.00699

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.00188

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.105 AC: 15904 AN: 151976 Hom.: 2666 Cov.: 32 AF XY: 0.102 AC XY: 7547 AN XY: 74286

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.0219

Gnomad4 FIN AF: 0.00699

Gnomad4 NFE AF: 0.00188

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0200 Hom.: 397

Bravo AF: 0.120

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	-0.79
CADD	Benign	1.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs793046; hg19: chr20-52962188;