ENST00000470726.7:n.346+103669T>G

Variant names:

• chr13-50537219-T-G
• rs3116602
• ENST00000469127.6:n.585+31539T>G

Variant summary

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

The ENST00000470726.7(DLEU1):​n.346+103669T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,220 control chromosomes in the GnomAD database, including 2,270 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 0.15 (2270 hom., cov: 32)
• Consequence: DLEU1 ENST00000470726.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 40 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470726.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.585+31539T>G		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+103669T>G		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.457+44458T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22945 AN: 152102 Hom.: 2271 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.151 AC: 22931 AN: 152220 Hom.: 2270 Cov.: 32 AF XY: 0.151 AC XY: 11241 AN XY: 74416

African (AFR) AF: 0.0370 AC: 1537 AN: 41552

American (AMR) AF: 0.153 AC: 2336 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3470

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5184

South Asian (SAS) AF: 0.0854 AC: 412 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2895 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14362 AN: 67996

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.186 Hom.: 10702

Bravo AF: 0.140

Asia WGS AF: 0.0500 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.82
PhyloP100		-0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs3116602; hg19: chr13-51111355;