chr20-56245733-G-A

Variant names:

• chr20-56245733-G-A
• rs6024730

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 0.249 in 152,162 control chromosomes in the GnomAD database, including 5,260 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 0.25 (5260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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: 0.249 AC: 37880 AN: 152044 Hom.: 5247 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.249 AC: 37933 AN: 152162 Hom.: 5260 Cov.: 32 AF XY: 0.249 AC XY: 18514 AN XY: 74402

African (AFR) AF: 0.376 AC: 15616 AN: 41488

American (AMR) AF: 0.161 AC: 2457 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1514 AN: 5180

South Asian (SAS) AF: 0.286 AC: 1382 AN: 4826

European-Finnish (FIN) AF: 0.202 AC: 2141 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13240 AN: 67996

Other (OTH) AF: 0.212 AC: 449 AN: 2114

Alfa AF: 0.209 Hom.: 2301

Bravo AF: 0.249

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.69
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs6024730; hg19: chr20-54820789;