rs115456333
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_203486.3(DLL3):c.1152G>A(p.Ala384=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00269 in 1,543,398 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A384A) has been classified as Likely benign.
Frequency
Consequence
NM_203486.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLL3 | NM_203486.3 | c.1152G>A | p.Ala384= | synonymous_variant | 7/9 | ENST00000356433.10 | |
DLL3 | NM_016941.4 | c.1152G>A | p.Ala384= | synonymous_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLL3 | ENST00000356433.10 | c.1152G>A | p.Ala384= | synonymous_variant | 7/9 | 2 | NM_203486.3 | P1 | |
DLL3 | ENST00000205143.4 | c.1152G>A | p.Ala384= | synonymous_variant | 7/8 | 1 | |||
DLL3 | ENST00000596614.5 | c.468G>A | p.Ala156= | synonymous_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0142 AC: 2153AN: 152038Hom.: 41 Cov.: 31
GnomAD3 exomes AF: 0.00303 AC: 434AN: 143154Hom.: 11 AF XY: 0.00254 AC XY: 200AN XY: 78852
GnomAD4 exome AF: 0.00143 AC: 1993AN: 1391246Hom.: 43 Cov.: 31 AF XY: 0.00123 AC XY: 848AN XY: 687682
GnomAD4 genome ? AF: 0.0142 AC: 2157AN: 152152Hom.: 41 Cov.: 31 AF XY: 0.0137 AC XY: 1021AN XY: 74398
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 31, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Spondylocostal dysostosis 1, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 28, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at