20-50503858-T-G

Variant names:

• chr20-50503858-T-G
• rs6020563

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.516 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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.486

Alfa AF: 0.483 Hom.: 8433

Bravo AF: 0.526

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6020563; hg19: chr20-49120395;