X-111312782-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001195553.2(DCX):c.947-46T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 1,133,172 control chromosomes in the GnomAD database, including 240 homozygotes. There are 6,864 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001195553.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCX | ENST00000636035.2 | c.947-46T>C | intron_variant | Intron 5 of 6 | 2 | NM_001195553.2 | ENSP00000490614.1 | |||
DCX | ENST00000356220.8 | c.947-46T>C | intron_variant | Intron 6 of 7 | 5 | ENSP00000348553.4 | ||||
DCX | ENST00000637453.1 | c.947-46T>C | intron_variant | Intron 5 of 6 | 5 | ENSP00000490357.1 | ||||
DCX | ENST00000637570.1 | c.932-46T>C | intron_variant | Intron 5 of 6 | 5 | ENSP00000490878.1 |
Frequencies
GnomAD3 genomes AF: 0.0133 AC: 1488AN: 111924Hom.: 20 Cov.: 23 AF XY: 0.0114 AC XY: 389AN XY: 34088
GnomAD3 exomes AF: 0.0137 AC: 2393AN: 174853Hom.: 18 AF XY: 0.0134 AC XY: 808AN XY: 60271
GnomAD4 exome AF: 0.0213 AC: 21758AN: 1021196Hom.: 220 Cov.: 22 AF XY: 0.0217 AC XY: 6475AN XY: 298512
GnomAD4 genome AF: 0.0133 AC: 1489AN: 111976Hom.: 20 Cov.: 23 AF XY: 0.0114 AC XY: 389AN XY: 34150
ClinVar
Submissions by phenotype
not specified Benign:2
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not provided Benign:2
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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at