20-57469128-A-G

Variant names:

• chr20-57469128-A-G
• rs6070116

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 0.221 in 152,106 control chromosomes in the GnomAD database, including 3,953 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 0.22 (3953 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33568 AN: 151988 Hom.: 3946 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.221 AC: 33598 AN: 152106 Hom.: 3953 Cov.: 33 AF XY: 0.222 AC XY: 16484 AN XY: 74356

African (AFR) AF: 0.163 AC: 6746 AN: 41482

American (AMR) AF: 0.182 AC: 2776 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1408 AN: 5182

South Asian (SAS) AF: 0.315 AC: 1514 AN: 4812

European-Finnish (FIN) AF: 0.228 AC: 2411 AN: 10574

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17310 AN: 67980

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.234 Hom.: 7390

Bravo AF: 0.212

Asia WGS AF: 0.291 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.30
DANN	Benign	0.68
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs6070116; hg19: chr20-56044184;