rs683954

Variant names:

• chr20-49893324-A-G
• rs683954

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 0.888 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.901

Alfa AF: 0.887 Hom.: 15524

Bravo AF: 0.887

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs683954; hg19: chr20-48509861;