rs10498720
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016356.5(DCDC2):c.348+361T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 449,126 control chromosomes in the GnomAD database, including 1,684 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.045 ( 355 hom., cov: 33)
Exomes 𝑓: 0.070 ( 1329 hom. )
Consequence
DCDC2
NM_016356.5 intron
NM_016356.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.111
Genes affected
DCDC2 (HGNC:18141): (doublecortin domain containing 2) This gene encodes a doublecortin domain-containing family member. The doublecortin domain has been demonstrated to bind tubulin and enhance microtubule polymerization. This family member is thought to function in neuronal migration where it may affect the signaling of primary cilia. Mutations in this gene have been associated with reading disability (RD) type 2, also referred to as developmental dyslexia. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC2 | NM_016356.5 | c.348+361T>G | intron_variant | ENST00000378454.8 | |||
DCDC2 | NM_001195610.2 | c.348+361T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC2 | ENST00000378454.8 | c.348+361T>G | intron_variant | 1 | NM_016356.5 | P1 | |||
DCDC2 | ENST00000436313.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0451 AC: 6860AN: 152186Hom.: 350 Cov.: 33
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GnomAD4 exome AF: 0.0700 AC: 20778AN: 296822Hom.: 1329 Cov.: 0 AF XY: 0.0773 AC XY: 12983AN XY: 167896
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GnomAD4 genome ? AF: 0.0451 AC: 6869AN: 152304Hom.: 355 Cov.: 33 AF XY: 0.0496 AC XY: 3690AN XY: 74466
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ClinVar
Not reported inComputational 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