20-54345649-C-T

Variant names:

• chr20-54345649-C-T
• rs793046

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.353 AC: 14610 AN: 41372

American (AMR) AF: 0.0344 AC: 526 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3470

East Asian (EAS) AF: 0.0551 AC: 286 AN: 5188

South Asian (SAS) AF: 0.0219 AC: 105 AN: 4800

European-Finnish (FIN) AF: 0.00699 AC: 74 AN: 10584

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.00188 AC: 128 AN: 67978

Other (OTH) AF: 0.0735 AC: 155 AN: 2108

Alfa AF: 0.0345 Hom.: 907

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
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs793046; hg19: chr20-52962188;