X-111330905-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001195553.2(DCX):c.945C>T(p.Asp315=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000339 in 1,210,120 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001195553.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCX | NM_001195553.2 | c.945C>T | p.Asp315= | splice_region_variant, synonymous_variant | 5/7 | ENST00000636035.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCX | ENST00000636035.2 | c.945C>T | p.Asp315= | splice_region_variant, synonymous_variant | 5/7 | 2 | NM_001195553.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112462Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34626
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183010Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67584
GnomAD4 exome AF: 0.0000364 AC: 40AN: 1097658Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 13AN XY: 363074
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112462Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34626
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at