dbSNP rs9596270: DLEU1:n.441-6628T>C (chr13-50268304-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000461527.7(DLEU1):n.441-6628T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 152,274 control chromosomes in the GnomAD database, including 307 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 0.060 ( 307 hom., cov: 32)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.766

Publications

21 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.443-121894T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.441-6628T>C	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7 link	n.441-70372T>C	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.441-121894T>C	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.0597

AC:

9091

AN:

152160

Hom.:

306

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0432

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.0471

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.000768

Gnomad SAS

AF:

0.0410

Gnomad FIN

AF:

0.0570

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0746

Gnomad OTH

AF:

0.0559

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

GnomAD4 genome

AF:

0.0597

AC:

9095

AN:

152274

Hom.:

307

Cov.:

AF XY:

0.0583

AC XY:

4344

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.0433

AC:

1800

AN:

41560

American (AMR)

AF:

0.0469

AC:

718

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

394

AN:

3470

East Asian (EAS)

AF:

0.000770

AC:

AN:

5194

South Asian (SAS)

AF:

0.0413

AC:

199

AN:

4822

European-Finnish (FIN)

AF:

0.0570

AC:

605

AN:

10622

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0746

AC:

5069

AN:

67990

Other (OTH)

AF:

0.0553

AC:

117

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

434

868

1303

1737

2171

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0677

Hom.:

616

Bravo

AF:

0.0576

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.70

PhyloP100

0.77

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