20-55121461-C-T

Variant names:

• chr20-55121461-C-T
• rs1028546

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 0.683 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.684 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

African (AFR) AF: 0.236 AC: 9774 AN: 41400

American (AMR) AF: 0.785 AC: 12004 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2893 AN: 3468

East Asian (EAS) AF: 0.852 AC: 4421 AN: 5190

South Asian (SAS) AF: 0.867 AC: 4189 AN: 4830

European-Finnish (FIN) AF: 0.856 AC: 9060 AN: 10590

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58943 AN: 67980

Other (OTH) AF: 0.731 AC: 1547 AN: 2116

Alfa AF: 0.815 Hom.: 98540

Bravo AF: 0.656

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.74
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1028546; hg19: chr20-53738000;