20-56058149-A-C

Variant names:

• chr20-56058149-A-C
• rs6069551

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 0.309 in 151,412 control chromosomes in the GnomAD database, including 8,411 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 0.31 (8411 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46713 AN: 151294 Hom.: 8390 Cov.: 30

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.309 AC: 46775 AN: 151412 Hom.: 8411 Cov.: 30 AF XY: 0.309 AC XY: 22826 AN XY: 73940

African (AFR) AF: 0.493 AC: 20310 AN: 41190

American (AMR) AF: 0.220 AC: 3357 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2384 AN: 5098

South Asian (SAS) AF: 0.297 AC: 1425 AN: 4800

European-Finnish (FIN) AF: 0.280 AC: 2905 AN: 10366

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15060 AN: 67950

Other (OTH) AF: 0.267 AC: 563 AN: 2110

Alfa AF: 0.242 Hom.: 4369

Bravo AF: 0.314

Asia WGS AF: 0.426 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6069551; hg19: chr20-54633205;