rs1786383

Variant names:

• chr21-20458574-A-G
• rs1786383

Your query was ambiguous. Multiple possible variants found:

• chr21-20458574-A-G
• chr21-20458574-A-T

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 0.829 in 151,872 control chromosomes in the GnomAD database, including 52,300 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 0.83 (52300 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.829 AC: 125733 AN: 151752 Hom.: 52251 Cov.: 30

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.829 AC: 125842 AN: 151872 Hom.: 52300 Cov.: 30 AF XY: 0.828 AC XY: 61452 AN XY: 74214

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.839

Alfa AF: 0.833 Hom.: 6186

Bravo AF: 0.836

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1786383; hg19: chr21-21830886;