chr10-77794057-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_004747.4(DLG5):c.5607G>A(p.Gln1869=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,614,208 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 35 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 34 hom. )
Consequence
DLG5
NM_004747.4 synonymous
NM_004747.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0780
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 10-77794057-C-T is Benign according to our data. Variant chr10-77794057-C-T is described in ClinVar as [Benign]. Clinvar id is 778464.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.078 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0108 (1642/152350) while in subpopulation AFR AF= 0.037 (1538/41580). AF 95% confidence interval is 0.0355. There are 35 homozygotes in gnomad4. There are 747 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1628 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG5 | NM_004747.4 | c.5607G>A | p.Gln1869= | synonymous_variant | 31/32 | ENST00000372391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.5607G>A | p.Gln1869= | synonymous_variant | 31/32 | 1 | NM_004747.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0107 AC: 1628AN: 152232Hom.: 33 Cov.: 33
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GnomAD3 exomes AF: 0.00266 AC: 668AN: 251454Hom.: 11 AF XY: 0.00201 AC XY: 273AN XY: 135904
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GnomAD4 exome AF: 0.00114 AC: 1662AN: 1461858Hom.: 34 Cov.: 32 AF XY: 0.00101 AC XY: 731AN XY: 727236
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GnomAD4 genome ? AF: 0.0108 AC: 1642AN: 152350Hom.: 35 Cov.: 33 AF XY: 0.0100 AC XY: 747AN XY: 74504
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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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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