Genetic Variant DLEU1:n.346+109215G>T (chr13-50542765-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000651397.1(DLEU7):n.*572-16758C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,900 control chromosomes in the GnomAD database, including 2,261 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 ( 2261 hom., cov: 31)

Consequence

DLEU7
ENST00000651397.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.616

Variant links:

Genes affected

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

DLEU1 links:

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

DLEU7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000470726.7 link	n.346+109215G>T	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-46710G>T	intron_variant	Intron 4 of 5	5
DLEU1	ENST00000484869.6 link	n.1329+39885G>T	intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22830

AN:

151780

Hom.:

2262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0352

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.0193

Gnomad SAS

AF:

0.0874

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.154

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.172

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

GnomAD4 genome

AF:

0.150

AC:

22816

AN:

151900

Hom.:

2261

Cov.:

AF XY:

0.151

AC XY:

11185

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.0351

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.178

Gnomad4 EAS

AF:

0.0194

Gnomad4 SAS

AF:

0.0864

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.211

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.194

Hom.:

4904

Bravo

AF:

0.139

Asia WGS

AF:

0.0500

AC:

178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.57

DANN

Benign

0.51

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over