dbSNP rs3118916: DLEU1:n.586-26803G>A (chr13-50562672-G-A) – 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.586-26803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,010 control chromosomes in the GnomAD database, including 2,195 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 ( 2195 hom., cov: 31)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.197

Publications

10 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:

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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 = 0.203 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.586-26803G>A	intron_variant	Intron 5 of 6	5
DLEU1	ENST00000470726.7 link	n.346+129122G>A	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-26803G>A	intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22452

AN:

151892

Hom.:

2196

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0368

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.0862

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.171

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

GnomAD4 genome

AF:

0.148

AC:

22439

AN:

152010

Hom.:

2195

Cov.:

AF XY:

0.148

AC XY:

11002

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.0366

AC:

1520

AN:

41476

American (AMR)

AF:

0.146

AC:

2223

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

654

AN:

3472

East Asian (EAS)

AF:

0.0211

AC:

109

AN:

5178

South Asian (SAS)

AF:

0.0853

AC:

411

AN:

4820

European-Finnish (FIN)

AF:

0.273

AC:

2876

AN:

10532

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

13978

AN:

67944

Other (OTH)

AF:

0.168

AC:

354

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

942

1884

2826

3768

4710

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.183

Hom.:

4935

Bravo

AF:

0.137

Asia WGS

AF:

0.0520

AC:

185

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

5.0

(source)

DANN

Benign

0.62

PhyloP100

-0.20

Splicing

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

Publications

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rs3118916

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