chr8-1548973-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001346810.2(DLGAP2):c.520G>A(p.Asp174Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,598,920 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 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. D174G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001346810.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP2 | NM_001346810.2 | c.520G>A | p.Asp174Asn | missense_variant | 5/15 | ENST00000637795.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP2 | ENST00000637795.2 | c.520G>A | p.Asp174Asn | missense_variant | 5/15 | 5 | NM_001346810.2 | ||
DLGAP2 | ENST00000520901.5 | c.331G>A | p.Asp111Asn | missense_variant | 1/10 | 1 | |||
DLGAP2 | ENST00000421627.7 | c.517G>A | p.Asp173Asn | missense_variant | 5/15 | 5 | |||
DLGAP2 | ENST00000612087.1 | c.280G>A | p.Asp94Asn | missense_variant | 2/11 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000132 AC: 3AN: 227758Hom.: 0 AF XY: 0.0000159 AC XY: 2AN XY: 125772
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1446686Hom.: 1 Cov.: 35 AF XY: 0.0000167 AC XY: 12AN XY: 720214
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 23, 2021 | The c.280G>A (p.D94N) alteration is located in exon 2 (coding exon 1) of the DLGAP2 gene. This alteration results from a G to A substitution at nucleotide position 280, causing the aspartic acid (D) at amino acid position 94 to be replaced by an asparagine (N). 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