X-70454271-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_021120.4(DLG3):c.1360C>T(p.Arg454Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 1,209,698 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021120.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000358 AC: 4AN: 111844Hom.: 0 Cov.: 24 AF XY: 0.0000588 AC XY: 2AN XY: 34040
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182629Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67087
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1097854Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363212
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111844Hom.: 0 Cov.: 24 AF XY: 0.0000588 AC XY: 2AN XY: 34040
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1360C>T (p.R454W) alteration is located in exon 9 (coding exon 9) of the DLG3 gene. This alteration results from a C to T substitution at nucleotide position 1360, causing the arginine (R) at amino acid position 454 to be replaced by a tryptophan (W). 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