18-3879209-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004746.4(DLGAP1):c.860G>A(p.Arg287Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000354 in 1,562,876 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_004746.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000708 AC: 150AN: 211976Hom.: 1 AF XY: 0.000935 AC XY: 106AN XY: 113344
GnomAD4 exome AF: 0.000366 AC: 516AN: 1410534Hom.: 9 Cov.: 31 AF XY: 0.000527 AC XY: 367AN XY: 696220
GnomAD4 genome AF: 0.000243 AC: 37AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74496
ClinVar
Submissions by phenotype
DLGAP1-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at