dbSNP rs201762: DLEU1:n.252-951T>G (chr13-50491700-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000460525.6(DLEU1):n.252-951T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,210 control chromosomes in the GnomAD database, including 2,475 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 0.16 ( 2475 hom., cov: 32)

Consequence

DLEU1
ENST00000460525.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336

Publications

7 publications found

Variant links:

Genes affected

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

DLEU1 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.675-951T>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000460525.6 link	n.252-951T>G	intron_variant	Intron 2 of 3	1
DLEU1	ENST00000461527.7 link	n.808-951T>G	intron_variant	Intron 5 of 5	1
DLEU1	ENST00000462427.2 link	n.253-36166T>G	intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24541

AN:

152092

Hom.:

2476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0541

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.0204

Gnomad SAS

AF:

0.0933

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.183

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

GnomAD4 genome

AF:

0.161

AC:

24534

AN:

152210

Hom.:

2475

Cov.:

AF XY:

0.161

AC XY:

11941

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.0540

AC:

2245

AN:

41554

American (AMR)

AF:

0.153

AC:

2341

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

648

AN:

3472

East Asian (EAS)

AF:

0.0202

AC:

105

AN:

5186

South Asian (SAS)

AF:

0.0925

AC:

446

AN:

4820

European-Finnish (FIN)

AF:

0.284

AC:

3008

AN:

10582

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.221

AC:

15045

AN:

67998

Other (OTH)

AF:

0.180

AC:

380

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1015

2029

3044

4058

5073

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.201

Hom.:

6375

Bravo

AF:

0.151

Asia WGS

AF:

0.0600

AC:

211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.7

(source)

DANN

Benign

0.77

PhyloP100

0.34

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