rs770389

chr13-50571020-G-A

Variant summary

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

The ENST00000651397.1(DLEU7):c.*572-45013C>T variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

Genes affected

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

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

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU7	ENST00000651397.1	c.*572-45013C>T		intron_variant, NMD_transcript_variant
DLEU1	ENST00000470726.7	n.346+137470G>A		intron_variant, non_coding_transcript_variant		5
DLEU1	ENST00000479420.5	n.458-18455G>A		intron_variant, non_coding_transcript_variant		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;