chr20-50449059-A-G

Variant names:

• chr20-50449059-A-G
• rs803742

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 0.49 in 151,068 control chromosomes in the GnomAD database, including 19,661 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 0.49 (19661 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.626 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: 0.490 AC: 74017 AN: 150958 Hom.: 19668 Cov.: 29

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.490 AC: 74038 AN: 151068 Hom.: 19661 Cov.: 29 AF XY: 0.494 AC XY: 36382 AN XY: 73704

African (AFR) AF: 0.271 AC: 11124 AN: 41056

American (AMR) AF: 0.637 AC: 9672 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1952 AN: 5086

South Asian (SAS) AF: 0.520 AC: 2495 AN: 4794

European-Finnish (FIN) AF: 0.620 AC: 6389 AN: 10306

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38647 AN: 67878

Other (OTH) AF: 0.516 AC: 1080 AN: 2094

Alfa AF: 0.537 Hom.: 4728

Bravo AF: 0.484

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.33
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs803742; hg19: chr20-49065596;