6-24357438-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000378454.8(DCDC2):c.293+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000012 in 1,580,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
DCDC2
ENST00000378454.8 intron
ENST00000378454.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0760
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 6-24357438-G-A is Benign according to our data. Variant chr6-24357438-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2142443.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCDC2 | NM_016356.5 | c.293+20C>T | intron_variant | ENST00000378454.8 | NP_057440.2 | |||
KAAG1 | NR_174942.1 | n.536G>A | non_coding_transcript_exon_variant | 1/1 | ||||
DCDC2 | NM_001195610.2 | c.293+20C>T | intron_variant | NP_001182539.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCDC2 | ENST00000378454.8 | c.293+20C>T | intron_variant | 1 | NM_016356.5 | ENSP00000367715 | P1 | |||
KAAG1 | ENST00000274766.2 | n.536G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
DCDC2 | ENST00000436313.1 | c.196+20C>T | intron_variant | 3 | ENSP00000410939 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000440 AC: 1AN: 227110Hom.: 0 AF XY: 0.00000822 AC XY: 1AN XY: 121684
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GnomAD4 exome AF: 0.0000119 AC: 17AN: 1427968Hom.: 0 Cov.: 30 AF XY: 0.0000127 AC XY: 9AN XY: 706062
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 66;C4479344:Isolated neonatal sclerosing cholangitis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 02, 2022 | - - |
Computational scores
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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