chr8-1548979-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001346810.2(DLGAP2):āc.526T>Cā(p.Cys176Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000108 in 1,599,326 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 Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C176F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001346810.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP2 | NM_001346810.2 | c.526T>C | p.Cys176Arg | missense_variant | 5/15 | ENST00000637795.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP2 | ENST00000637795.2 | c.526T>C | p.Cys176Arg | missense_variant | 5/15 | 5 | NM_001346810.2 | ||
DLGAP2 | ENST00000520901.5 | c.337T>C | p.Cys113Arg | missense_variant | 1/10 | 1 | |||
DLGAP2 | ENST00000421627.7 | c.523T>C | p.Cys175Arg | missense_variant | 5/15 | 5 | |||
DLGAP2 | ENST00000612087.1 | c.286T>C | p.Cys96Arg | missense_variant | 2/11 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000657 AC: 15AN: 228444Hom.: 0 AF XY: 0.0000396 AC XY: 5AN XY: 126118
GnomAD4 exome AF: 0.0000857 AC: 124AN: 1446994Hom.: 0 Cov.: 35 AF XY: 0.0000861 AC XY: 62AN XY: 720334
GnomAD4 genome AF: 0.000322 AC: 49AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.286T>C (p.C96R) alteration is located in exon 2 (coding exon 1) of the DLGAP2 gene. This alteration results from a T to C substitution at nucleotide position 286, causing the cysteine (C) at amino acid position 96 to be replaced by an arginine (R). 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