rs6066563

Variant names:

• chr20-47949975-A-G
• rs6066563

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 0.194 in 152,166 control chromosomes in the GnomAD database, including 3,020 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 0.19 (3020 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 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: 0.194 AC: 29545 AN: 152048 Hom.: 3012 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.194 AC: 29587 AN: 152166 Hom.: 3020 Cov.: 32 AF XY: 0.200 AC XY: 14856 AN XY: 74398

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.178

Alfa AF: 0.179 Hom.: 5328

Bravo AF: 0.179

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6066563; hg19: chr20-46578719;