20-49975221-G-A

Variant names:

• chr20-49975221-G-A
• rs6020157

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 0.282 in 151,582 control chromosomes in the GnomAD database, including 7,722 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 0.28 (7722 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 12 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 (AFR) allele frequency at 95% confidence interval = 0.508 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: 0.282 AC: 42683 AN: 151470 Hom.: 7706 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.282 AC: 42745 AN: 151582 Hom.: 7722 Cov.: 31 AF XY: 0.277 AC XY: 20503 AN XY: 74024

African (AFR) AF: 0.514 AC: 21253 AN: 41344

American (AMR) AF: 0.288 AC: 4394 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1359 AN: 5098

South Asian (SAS) AF: 0.162 AC: 779 AN: 4804

European-Finnish (FIN) AF: 0.135 AC: 1408 AN: 10418

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11869 AN: 67916

Other (OTH) AF: 0.289 AC: 606 AN: 2100

Alfa AF: 0.209 Hom.: 11675

Bravo AF: 0.307

Asia WGS AF: 0.225 AC: 783 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	2.9
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6020157; hg19: chr20-48591758;