chr20-50503858-T-G

Variant names:

• chr20-50503858-T-G
• rs6020563

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 0.516 in 151,984 control chromosomes in the GnomAD database, including 20,884 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 0.52 (20884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78323 AN: 151866 Hom.: 20848 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.516 AC: 78415 AN: 151984 Hom.: 20884 Cov.: 32 AF XY: 0.512 AC XY: 38047 AN XY: 74258

African (AFR) AF: 0.659 AC: 27279 AN: 41424

American (AMR) AF: 0.489 AC: 7466 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1553 AN: 5168

South Asian (SAS) AF: 0.370 AC: 1786 AN: 4824

European-Finnish (FIN) AF: 0.447 AC: 4713 AN: 10542

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32484 AN: 67960

Other (OTH) AF: 0.486 AC: 1027 AN: 2112

Alfa AF: 0.483 Hom.: 9286

Bravo AF: 0.526

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.54
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6020563; hg19: chr20-49120395;