chr20-43666053-C-T

Variant names:

• chr20-43666053-C-T
• rs826943

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 0.81 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.810 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

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.800

Alfa AF: 0.844 Hom.: 6392

Bravo AF: 0.792

Asia WGS AF: 0.784 AC: 2726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826943; hg19: chr20-42294693;