8-907927-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001346810.2(DLGAP2):c.34C>T(p.Leu12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000346 in 398,978 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 (no stars).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00036 ( 0 hom. )
Consequence
DLGAP2
NM_001346810.2 synonymous
NM_001346810.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.97
Genes affected
DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.19).
BP6
Variant 8-907927-C-T is Benign according to our data. Variant chr8-907927-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3044500.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.97 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| DLGAP2 | NM_001346810.2 | c.34C>T | p.Leu12= | synonymous_variant | 2/15 | ENST00000637795.2 | |
| DLGAP2 | NR_073397.2 | n.316C>T | non_coding_transcript_exon_variant | 3/4 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DLGAP2 | ENST00000637795.2 | c.34C>T | p.Leu12= | synonymous_variant | 2/15 | 5 | NM_001346810.2 |
Frequencies
GnomAD3 genomes 0.000322 AC: 49AN: 152230Hom.: 0 Cov.: 34
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GnomAD4 exome AF: 0.000361 AC: 89AN: 246630Hom.: 0 Cov.: 0 AF XY: 0.000320 AC XY: 40AN XY: 124984
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GnomAD4 genome 0.000322 AC: 49AN: 152348Hom.: 0 Cov.: 34 AF XY: 0.000282 AC XY: 21AN XY: 74498
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
DLGAP2-related disorder Benign:1
| Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 31, 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
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Benign
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Benign
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Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at