chr8-1549272-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001346810.2(DLGAP2):c.819G>A(p.Lys273=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,459,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001346810.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP2 | NM_001346810.2 | c.819G>A | p.Lys273= | synonymous_variant | 5/15 | ENST00000637795.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP2 | ENST00000637795.2 | c.819G>A | p.Lys273= | synonymous_variant | 5/15 | 5 | NM_001346810.2 | ||
DLGAP2 | ENST00000520901.5 | c.630G>A | p.Lys210= | synonymous_variant | 1/10 | 1 | |||
DLGAP2 | ENST00000421627.7 | c.816G>A | p.Lys272= | synonymous_variant | 5/15 | 5 | |||
DLGAP2 | ENST00000612087.1 | c.579G>A | p.Lys193= | synonymous_variant | 2/11 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459020Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 725970
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
DLGAP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 05, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.