rs6053189

Variant names:

• chr20-5198933-A-G
• rs6053189

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 0.309 in 152,122 control chromosomes in the GnomAD database, including 7,760 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 0.31 (7760 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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: 0.309 AC: 46913 AN: 152004 Hom.: 7754 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.309 AC: 46935 AN: 152122 Hom.: 7760 Cov.: 33 AF XY: 0.305 AC XY: 22675 AN XY: 74350

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.305

Alfa AF: 0.336 Hom.: 1083

Bravo AF: 0.296

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6053189; hg19: chr20-5179579;