20-36439758-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001365621.2(DLGAP4):c.1246C>A(p.Leu416Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365621.2 missense
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 |
---|---|---|---|---|---|---|---|
DLGAP4 | NM_001365621.2 | c.1246C>A | p.Leu416Met | missense_variant | 5/13 | ENST00000339266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP4 | ENST00000339266.10 | c.1246C>A | p.Leu416Met | missense_variant | 5/13 | 5 | NM_001365621.2 | ||
DLGAP4 | ENST00000373913.7 | c.1246C>A | p.Leu416Met | missense_variant | 5/13 | 1 | |||
DLGAP4 | ENST00000373907.6 | c.1246C>A | p.Leu416Met | missense_variant | 4/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249600Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134972
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460580Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726596
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1246C>A (p.L416M) alteration is located in exon 4 (coding exon 3) of the DLGAP4 gene. This alteration results from a C to A substitution at nucleotide position 1246, causing the leucine (L) at amino acid position 416 to be replaced by a methionine (M). 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