20-54084754-C-T

Position:

• chr20-54084754-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 0.418 in 152,142 control chromosomes in the GnomAD database, including 14,736 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 0.42 (14736 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54084754C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63551 AN: 152022 Hom.: 14728 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.418 AC: 63574 AN: 152142 Hom.: 14736 Cov.: 33 AF XY: 0.416 AC XY: 30921 AN XY: 74390

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.482

Alfa AF: 0.497 Hom.: 39243

Bravo AF: 0.428

Asia WGS AF: 0.302 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6064045; hg19: chr20-52701293;