20-43666053-C-T

Variant names:

• chr20-43666053-C-T
• rs826943

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 0.81 in 149,926 control chromosomes in the GnomAD database, including 49,862 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 0.81 (49862 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 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: 0.810 AC: 121411 AN: 149804 Hom.: 49838 Cov.: 24

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.810 AC: 121483 AN: 149926 Hom.: 49862 Cov.: 24 AF XY: 0.813 AC XY: 59342 AN XY: 73020

African (AFR) AF: 0.678 AC: 27495 AN: 40536

American (AMR) AF: 0.789 AC: 11837 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2942 AN: 3468

East Asian (EAS) AF: 0.798 AC: 4050 AN: 5074

South Asian (SAS) AF: 0.821 AC: 3910 AN: 4764

European-Finnish (FIN) AF: 0.918 AC: 9259 AN: 10086

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59310 AN: 67738

Other (OTH) AF: 0.800 AC: 1654 AN: 2068

Alfa AF: 0.837 Hom.: 6570

Bravo AF: 0.792

Asia WGS AF: 0.784 AC: 2726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs826943; hg19: chr20-42294693;