Genetic Variant ENST00000469127.6:n.688-18200C>T (chr13-50620269-C-T) – 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.688-18200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,004 control chromosomes in the GnomAD database, including 7,379 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 0.30 ( 7379 hom., cov: 32)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.837

Publications

13 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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.688-18200C>T	intron_variant	Intron 6 of 6	5
DLEU1	ENST00000470726.7 link	n.347-99378C>T	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.560-28321C>T	intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

46067

AN:

151886

Hom.:

7379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.333

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

GnomAD4 genome

AF:

0.303

AC:

46084

AN:

152004

Hom.:

7379

Cov.:

AF XY:

0.304

AC XY:

22569

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.212

AC:

8789

AN:

41462

American (AMR)

AF:

0.341

AC:

5203

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

1110

AN:

3468

East Asian (EAS)

AF:

0.243

AC:

1257

AN:

5176

South Asian (SAS)

AF:

0.226

AC:

1088

AN:

4812

European-Finnish (FIN)

AF:

0.374

AC:

3943

AN:

10552

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.347

AC:

23595

AN:

67948

Other (OTH)

AF:

0.331

AC:

699

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1606

3212

4817

6423

8029

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.334

Hom.:

37949

Bravo

AF:

0.300

Asia WGS

AF:

0.226

AC:

789

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

0.12

(source)

DANN

Benign

0.65

PhyloP100

-0.84

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