rs1248688
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004747.4(DLG5):c.864+2059C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,176 control chromosomes in the GnomAD database, including 5,494 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 0.25 ( 5494 hom., cov: 33)
Consequence
DLG5
NM_004747.4 intron
NM_004747.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.178
Publications
5 publications found
Genes affected
DLG5 (HGNC:2904): (discs large MAGUK scaffold protein 5) This gene encodes a member of the family of discs large (DLG) homologs, a subset of the membrane-associated guanylate kinase (MAGUK) superfamily. The MAGUK proteins are composed of a catalytically inactive guanylate kinase domain, in addition to PDZ and SH3 domains, and are thought to function as scaffolding molecules at sites of cell-cell contact. The protein encoded by this gene localizes to the plasma membrane and cytoplasm, and interacts with components of adherens junctions and the cytoskeleton. It is proposed to function in the transmission of extracellular signals to the cytoskeleton and in the maintenance of epithelial cell structure. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]
DLG5 Gene-Disease associations (from GenCC):
- Yuksel-Vogel-Bauer syndromeInheritance: AD, AR Classification: LIMITED Submitted by: G2P
- ciliopathyInheritance: AR, AD Classification: LIMITED Submitted by: Franklin by Genoox
- congenital anomaly of kidney and urinary tractInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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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=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.864+2059C>T | intron_variant | Intron 5 of 31 | 1 | NM_004747.4 | ENSP00000361467.2 | |||
DLG5 | ENST00000468332.6 | n.639+2059C>T | intron_variant | Intron 5 of 29 | 2 | ENSP00000473298.1 | ||||
DLG5 | ENST00000475613.6 | n.93+17804C>T | intron_variant | Intron 1 of 21 | 5 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38694AN: 152058Hom.: 5486 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
38694
AN:
152058
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.254 AC: 38708AN: 152176Hom.: 5494 Cov.: 33 AF XY: 0.260 AC XY: 19308AN XY: 74384 show subpopulations
GnomAD4 genome
AF:
AC:
38708
AN:
152176
Hom.:
Cov.:
33
AF XY:
AC XY:
19308
AN XY:
74384
show subpopulations
African (AFR)
AF:
AC:
6270
AN:
41536
American (AMR)
AF:
AC:
5916
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
616
AN:
3472
East Asian (EAS)
AF:
AC:
1597
AN:
5178
South Asian (SAS)
AF:
AC:
1447
AN:
4830
European-Finnish (FIN)
AF:
AC:
3270
AN:
10570
Middle Eastern (MID)
AF:
AC:
71
AN:
294
European-Non Finnish (NFE)
AF:
AC:
18861
AN:
67986
Other (OTH)
AF:
AC:
500
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1465
2930
4395
5860
7325
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
400
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2000
<30
30-35
35-40
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1119
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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