10-77796543-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004747.4(DLG5):c.5216T>C(p.Leu1739Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00199 in 1,614,154 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 25 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 25 hom. )
Consequence
DLG5
NM_004747.4 missense
NM_004747.4 missense
Scores
2
13
Clinical Significance
Conservation
PhyloP100: 4.51
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0064600706).
BP6
?
Variant 10-77796543-A-G is Benign according to our data. Variant chr10-77796543-A-G is described in ClinVar as [Benign]. Clinvar id is 776519.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0103 (1574/152326) while in subpopulation AFR AF= 0.0355 (1474/41566). AF 95% confidence interval is 0.034. There are 25 homozygotes in gnomad4. There are 737 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1564 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG5 | NM_004747.4 | c.5216T>C | p.Leu1739Pro | missense_variant | 28/32 | ENST00000372391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.5216T>C | p.Leu1739Pro | missense_variant | 28/32 | 1 | NM_004747.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1564AN: 152208Hom.: 25 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00264 AC: 664AN: 251078Hom.: 8 AF XY: 0.00195 AC XY: 264AN XY: 135726
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GnomAD4 exome AF: 0.00112 AC: 1635AN: 1461828Hom.: 25 Cov.: 32 AF XY: 0.000968 AC XY: 704AN XY: 727214
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GnomAD4 genome ? AF: 0.0103 AC: 1574AN: 152326Hom.: 25 Cov.: 33 AF XY: 0.00989 AC XY: 737AN XY: 74484
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150
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410
Asia WGS
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11
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.0010
.;B
Vest4
0.26
MVP
MPC
0.38
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at