rs770389

Variant names:

• chr13-50571020-G-A
• rs770389
• ENST00000470726.7:n.346+137470G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-50571020-G-A
• chr13-50571020-G-C
• chr13-50571020-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651397.1(DLEU7):​n.*572-45013C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,046 control chromosomes in the GnomAD database, including 2,825 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 0.19 (2825 hom., cov: 31)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

Genes affected

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 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
DLEU1	ENST00000470726.7	n.346+137470G>A		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5	n.458-18455G>A		intron_variant	Intron 4 of 5	5
DLEU1	ENST00000484869.6	n.1330-60257G>A		intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28778 AN: 151926 Hom.: 2823 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.189 AC: 28786 AN: 152046 Hom.: 2825 Cov.: 31 AF XY: 0.189 AC XY: 14017 AN XY: 74298

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.210

Alfa AF: 0.201 Hom.: 4325

Bravo AF: 0.188

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs770389; hg19: chr13-51145156;