rs6066563

Positions:

• chr20-47949975-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;