rs683954

Variant names:

• chr20-49893324-A-G
• rs683954

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 0.888 in 152,282 control chromosomes in the GnomAD database, including 60,168 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 0.89 (60168 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.888 AC: 135190 AN: 152164 Hom.: 60129 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.888 AC: 135286 AN: 152282 Hom.: 60168 Cov.: 33 AF XY: 0.891 AC XY: 66338 AN XY: 74456

African (AFR) AF: 0.857 AC: 35617 AN: 41552

American (AMR) AF: 0.920 AC: 14089 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 2998 AN: 3466

East Asian (EAS) AF: 0.964 AC: 4990 AN: 5178

South Asian (SAS) AF: 0.919 AC: 4437 AN: 4826

European-Finnish (FIN) AF: 0.919 AC: 9754 AN: 10612

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60407 AN: 68024

Other (OTH) AF: 0.901 AC: 1904 AN: 2114

Alfa AF: 0.890 Hom.: 25519

Bravo AF: 0.887

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.092
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs683954; hg19: chr20-48509861;