rs1884389

Variant names:

• chr20-1429938-C-T
• rs1884389

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 0.419 in 151,986 control chromosomes in the GnomAD database, including 14,052 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 0.42 (14052 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.419 AC: 63676 AN: 151866 Hom.: 14046 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.419 AC: 63705 AN: 151986 Hom.: 14052 Cov.: 33 AF XY: 0.421 AC XY: 31258 AN XY: 74286

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.411

Alfa AF: 0.431 Hom.: 6228

Bravo AF: 0.423

Asia WGS AF: 0.579 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884389; hg19: chr20-1410582;