chr10-77805761-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004747.4(DLG5):c.5068C>T(p.Arg1690Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1690Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_004747.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG5 | NM_004747.4 | c.5068C>T | p.Arg1690Trp | missense_variant | 27/32 | ENST00000372391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG5 | ENST00000372391.7 | c.5068C>T | p.Arg1690Trp | missense_variant | 27/32 | 1 | NM_004747.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251352Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135870
GnomAD4 exome AF: 0.000172 AC: 251AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.000168 AC XY: 122AN XY: 727240
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.5068C>T (p.R1690W) alteration is located in exon 27 (coding exon 27) of the DLG5 gene. This alteration results from a C to T substitution at nucleotide position 5068, causing the arginine (R) at amino acid position 1690 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at