rs6066563

Variant names:

• chr20-47949975-A-G
• rs6066563

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 0.194 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.194 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

African (AFR) AF: 0.218 AC: 9065 AN: 41490

American (AMR) AF: 0.114 AC: 1749 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1451 AN: 5180

South Asian (SAS) AF: 0.353 AC: 1702 AN: 4822

European-Finnish (FIN) AF: 0.230 AC: 2437 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11994 AN: 68006

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.182 Hom.: 11489

Bravo AF: 0.179

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs6066563; hg19: chr20-46578719;