dbSNP rs1853926: DLEU1:n.440+68862G>C (chr13-50152056-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000461527.7(DLEU1):n.440+68862G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0265 in 151,032 control chromosomes in the GnomAD database, including 102 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 0.026 ( 102 hom., cov: 31)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250

Publications

1 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.442+68862G>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.440+68862G>C	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7 link	n.440+68862G>C	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.440+68862G>C	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.0264

AC:

3989

AN:

150916

Hom.:

101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0611

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0207

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00461

Gnomad FIN

AF:

0.0107

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0134

Gnomad OTH

AF:

0.0252

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

GnomAD4 genome

AF:

0.0265

AC:

4000

AN:

151032

Hom.:

102

Cov.:

AF XY:

0.0258

AC XY:

1899

AN XY:

73706

show subpopulations

African (AFR)

AF:

0.0611

AC:

2516

AN:

41168

American (AMR)

AF:

0.0208

AC:

314

AN:

15108

Ashkenazi Jewish (ASJ)

AF:

0.0202

AC:

AN:

3464

East Asian (EAS)

AF:

0.000195

AC:

AN:

5118

South Asian (SAS)

AF:

0.00482

AC:

AN:

4770

European-Finnish (FIN)

AF:

0.0107

AC:

110

AN:

10294

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0134

AC:

908

AN:

67818

Other (OTH)

AF:

0.0249

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

195

390

586

781

976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.0201

Hom.:

Bravo

AF:

0.0286

Asia WGS

AF:

0.00694

AC:

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.3

(source)

DANN

Benign

0.38

PhyloP100

0.25

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