20-50469580-G-A

Variant names:

• chr20-50469580-G-A
• rs4811072

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 0.798 in 151,998 control chromosomes in the GnomAD database, including 49,102 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 0.80 (49102 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 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: 0.798 AC: 121231 AN: 151880 Hom.: 49056 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.798 AC: 121327 AN: 151998 Hom.: 49102 Cov.: 30 AF XY: 0.799 AC XY: 59358 AN XY: 74272

African (AFR) AF: 0.919 AC: 38092 AN: 41462

American (AMR) AF: 0.825 AC: 12602 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2626 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2849 AN: 5148

South Asian (SAS) AF: 0.811 AC: 3898 AN: 4806

European-Finnish (FIN) AF: 0.795 AC: 8401 AN: 10568

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50338 AN: 67968

Other (OTH) AF: 0.775 AC: 1637 AN: 2112

Alfa AF: 0.765 Hom.: 123228

Bravo AF: 0.805

Asia WGS AF: 0.712 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4811072; hg19: chr20-49086117;