rs61036541
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001195553.2(DCX):c.705+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0058 in 1,175,072 control chromosomes in the GnomAD database, including 70 homozygotes. There are 2,072 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 35 hom., 481 hem., cov: 23)
Exomes 𝑓: 0.0046 ( 35 hom. 1591 hem. )
Consequence
DCX
NM_001195553.2 intron
NM_001195553.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0250
Genes affected
DCX (HGNC:2714): (doublecortin) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a cytoplasmic protein and contains two doublecortin domains, which bind microtubules. In the developing cortex, cortical neurons must migrate over long distances to reach the site of their final differentiation. The encoded protein appears to direct neuronal migration by regulating the organization and stability of microtubules. In addition, the encoded protein interacts with LIS1, the regulatory gamma subunit of platelet activating factor acetylhydrolase, and this interaction is important to proper microtubule function in the developing cortex. Mutations in this gene cause abnormal migration of neurons during development and disrupt the layering of the cortex, leading to epilepsy, cognitive disability, subcortical band heterotopia ("double cortex" syndrome) in females and lissencephaly ("smooth brain" syndrome) in males. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant X-111400961-C-T is Benign according to our data. Variant chrX-111400961-C-T is described in ClinVar as [Benign]. Clinvar id is 262925.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111400961-C-T is described in Lovd as [Benign].
BA1
?
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0539 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCX | NM_001195553.2 | c.705+29G>A | intron_variant | ENST00000636035.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCX | ENST00000636035.2 | c.705+29G>A | intron_variant | 2 | NM_001195553.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0169 AC: 1899AN: 112089Hom.: 35 Cov.: 23 AF XY: 0.0139 AC XY: 478AN XY: 34293
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GnomAD3 exomes AF: 0.00713 AC: 1271AN: 178369Hom.: 20 AF XY: 0.00602 AC XY: 391AN XY: 64973
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GnomAD4 exome AF: 0.00462 AC: 4914AN: 1062928Hom.: 35 Cov.: 26 AF XY: 0.00477 AC XY: 1591AN XY: 333760
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GnomAD4 genome ? AF: 0.0169 AC: 1899AN: 112144Hom.: 35 Cov.: 23 AF XY: 0.0140 AC XY: 481AN XY: 34358
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at