20-46831684-G-A

Variant names:

• chr20-46831684-G-A
• rs6066084

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 0.504 in 152,076 control chromosomes in the GnomAD database, including 21,914 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 0.50 (21914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76566 AN: 151958 Hom.: 21908 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.504 AC: 76601 AN: 152076 Hom.: 21914 Cov.: 32 AF XY: 0.497 AC XY: 36917 AN XY: 74354

African (AFR) AF: 0.281 AC: 11636 AN: 41466

American (AMR) AF: 0.455 AC: 6953 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.0888 AC: 460 AN: 5180

South Asian (SAS) AF: 0.367 AC: 1767 AN: 4820

European-Finnish (FIN) AF: 0.644 AC: 6806 AN: 10566

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44909 AN: 67968

Other (OTH) AF: 0.501 AC: 1057 AN: 2108

Alfa AF: 0.597 Hom.: 73620

Bravo AF: 0.479

Asia WGS AF: 0.229 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.83
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6066084; hg19: chr20-45460323;