chr10-77805813-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004747.4(DLG5):c.5016T>C(p.Asp1672=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00354 in 1,614,148 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0037 ( 18 hom. )
Consequence
DLG5
NM_004747.4 synonymous
NM_004747.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.820
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 10-77805813-A-G is Benign according to our data. Variant chr10-77805813-A-G is described in ClinVar as [Benign]. Clinvar id is 718501.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.82 with no splicing effect.
BS2
?
High AC in GnomAd at 286 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG5 | NM_004747.4 | c.5016T>C | p.Asp1672= | synonymous_variant | 27/32 | ENST00000372391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.5016T>C | p.Asp1672= | synonymous_variant | 27/32 | 1 | NM_004747.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00188 AC: 286AN: 152202Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00215 AC: 539AN: 251274Hom.: 2 AF XY: 0.00217 AC XY: 295AN XY: 135794
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GnomAD4 exome AF: 0.00371 AC: 5428AN: 1461828Hom.: 18 Cov.: 31 AF XY: 0.00367 AC XY: 2667AN XY: 727204
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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 | Apr 03, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at