Genetic Variant ENST00000469127.6:n.687+16603A>G (chr13-50606179-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000469127.6(DLEU1):n.687+16603A>G 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

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449

Publications

7 publications found

Variant links:

Genes affected

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

DLEU1 links:

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

DLEU7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	ENST00000469127.6 link	n.687+16603A>G	intron_variant	Intron 6 of 6	5
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

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

African (AFR)

AF:

0.689

AC:

28573

AN:

41444

American (AMR)

AF:

0.503

AC:

7683

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.564

AC:

1955

AN:

3468

East Asian (EAS)

AF:

0.451

AC:

2331

AN:

5170

South Asian (SAS)

AF:

0.608

AC:

2927

AN:

4814

European-Finnish (FIN)

AF:

0.470

AC:

4955

AN:

10538

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.515

AC:

34973

AN:

67954

Other (OTH)

AF:

0.530

AC:

1121

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1848

3696

5543

7391

9239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.44

PhyloP100

-0.45

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over