chr20-54345649-C-T

Variant names:

• chr20-54345649-C-T
• rs793046

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;