rs587779754

chr20-7882896-A-Gchr20-7882896-A-T

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 0.0882 in 152,366 control chromosomes in the GnomAD database, including 1,289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.088 (1288 hom., cov: 33)
  • Exomes 𝑓: 0.036 (1 hom.)
• Consequence: Unknown
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 0.706

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13418 AN: 152164 Hom.: 1286 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0727

GnomAD4 exome AF: 0.0357 AC: 3 AN: 84 Hom.: 1 AF XY: 0.0400 AC XY: 2 AN XY: 50

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0883 AC: 13443 AN: 152282 Hom.: 1288 Cov.: 33 AF XY: 0.0906 AC XY: 6745 AN XY: 74458

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.0269

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0585 Hom.: 84

Bravo AF: 0.101

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Calcium oxalate urolithiasis Other:1

association, no assertion criteria provided

case-control

Division of Molecular Genetics and Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University

Mar 01, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.5
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6055363; hg19: chr20-7863543;