rs1884389

Variant names:

• chr20-1429938-C-T
• rs1884389
• ENST00000740734.1:n.124+5020G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000740734.1(ENSG00000296607):​n.124+5020G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000296607 ENST00000740734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 18 publications found

Genes affected

ENSG00000296607 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000296607	ENST00000740734.1	n.124+5020G>A		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.314 AC: 12996 AN: 41436

American (AMR) AF: 0.495 AC: 7559 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1418 AN: 3462

East Asian (EAS) AF: 0.786 AC: 4070 AN: 5176

South Asian (SAS) AF: 0.447 AC: 2155 AN: 4820

European-Finnish (FIN) AF: 0.414 AC: 4364 AN: 10542

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29762 AN: 67966

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.430 Hom.: 6905

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1884389; hg19: chr20-1410582;