Genetic Variant DLEU1:n.347-113468A>G (chr13-50606179-A-G) – 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.*571+77727T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,988 control chromosomes in the GnomAD database, including 24,484 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 0.56 ( 24484 hom., cov: 31)

Consequence

DLEU7
ENST00000651397.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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.347-113468A>G	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.559+16603A>G	intron_variant	Intron 5 of 5	5
DLEU1	ENST00000484869.6 link	n.1330-25098A>G	intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85030

AN:

151870

Hom.:

24454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.690

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.564

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.608

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.527

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

GnomAD4 genome

AF:

0.560

AC:

85111

AN:

151988

Hom.:

24484

Cov.:

AF XY:

0.557

AC XY:

41376

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.689

Gnomad4 AMR

AF:

0.503

Gnomad4 ASJ

AF:

0.564

Gnomad4 EAS

AF:

0.451

Gnomad4 SAS

AF:

0.608

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.515

Gnomad4 OTH

AF:

0.530

Alfa

AF:

0.540

Hom.:

2799

Bravo

AF:

0.561

Asia WGS

AF:

0.592

AC:

2055

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.40

DANN

Benign

0.44

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