dbSNP rs17074558: DLEU1:n.346+110763G>A (chr13-50544313-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000651397.1(DLEU7):n.*572-18306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,106 control chromosomes in the GnomAD database, including 432 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 0.069 ( 432 hom., cov: 32)

Consequence

DLEU7
ENST00000651397.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.70

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0852 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	ENST00000470726.7 link	n.346+110763G>A	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-45162G>A	intron_variant	Intron 4 of 5	5
DLEU1	ENST00000484869.6 link	n.1329+41433G>A	intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes

AF:

0.0694

AC:

10548

AN:

151986

Hom.:

431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0574

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0498

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.0187

Gnomad SAS

AF:

0.0914

Gnomad FIN

AF:

0.0701

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0826

Gnomad OTH

AF:

0.0737

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

GnomAD4 genome

AF:

0.0695

AC:

10565

AN:

152106

Hom.:

432

Cov.:

AF XY:

0.0689

AC XY:

5124

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.0572

Gnomad4 AMR

AF:

0.0498

Gnomad4 ASJ

AF:

0.0956

Gnomad4 EAS

AF:

0.0191

Gnomad4 SAS

AF:

0.0923

Gnomad4 FIN

AF:

0.0701

Gnomad4 NFE

AF:

0.0826

Gnomad4 OTH

AF:

0.0799

Alfa

AF:

0.0822

Hom.:

328

Bravo

AF:

0.0663

Asia WGS

AF:

0.0910

AC:

316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.77

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over