20-43666053-C-T

Position:

• chr20-43666053-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;