chr18-3534226-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004746.4(DLGAP1):c.2447G>A(p.Arg816Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0224 in 1,614,058 control chromosomes in the GnomAD database, including 482 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R816W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004746.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP1 | NM_004746.4 | c.2447G>A | p.Arg816Gln | missense_variant | 10/13 | ENST00000315677.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP1 | ENST00000315677.8 | c.2447G>A | p.Arg816Gln | missense_variant | 10/13 | 5 | NM_004746.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0164 AC: 2494AN: 152174Hom.: 34 Cov.: 32
GnomAD3 exomes AF: 0.0155 AC: 3898AN: 250866Hom.: 50 AF XY: 0.0155 AC XY: 2102AN XY: 135562
GnomAD4 exome AF: 0.0230 AC: 33659AN: 1461766Hom.: 448 Cov.: 33 AF XY: 0.0225 AC XY: 16326AN XY: 727178
GnomAD4 genome ? AF: 0.0164 AC: 2493AN: 152292Hom.: 34 Cov.: 32 AF XY: 0.0149 AC XY: 1112AN XY: 74464
ClinVar
Submissions by phenotype
DLGAP1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 08, 2019 | This variant is classified as 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