20-55121461-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 0.683 in 152,064 control chromosomes in the GnomAD database, including 41,348 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 0.68 (41348 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103893 AN: 151946 Hom.: 41369 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.683 AC: 103868 AN: 152064 Hom.: 41348 Cov.: 33 AF XY: 0.690 AC XY: 51278 AN XY: 74340

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.731

Alfa AF: 0.831 Hom.: 74281

Bravo AF: 0.656

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.9
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1028546; hg19: chr20-53738000;