20-56253273-T-G

Variant names:

• chr20-56253273-T-G
• rs1543873

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 0.274 in 152,110 control chromosomes in the GnomAD database, including 8,637 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 0.27 (8637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41516 AN: 151992 Hom.: 8602 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.274 AC: 41614 AN: 152110 Hom.: 8637 Cov.: 32 AF XY: 0.275 AC XY: 20434 AN XY: 74370

African (AFR) AF: 0.583 AC: 24146 AN: 41450

American (AMR) AF: 0.214 AC: 3273 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1395 AN: 5172

South Asian (SAS) AF: 0.264 AC: 1271 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2135 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8113 AN: 68010

Other (OTH) AF: 0.218 AC: 461 AN: 2110

Alfa AF: 0.166 Hom.: 4910

Bravo AF: 0.284

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.55
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1543873; hg19: chr20-54828329;