20-46831684-G-A

Position:

• chr20-46831684-G-A

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 0.504 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.504 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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.0888

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.501

Alfa AF: 0.607 Hom.: 22855

Bravo AF: 0.479

Asia WGS AF: 0.229 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6066084; hg19: chr20-45460323;