rs752971070
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_016008.4(DYNC2LI1):c.655-9delT variant causes a intron change. The variant allele was found at a frequency of 0.000022 in 1,500,608 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
DYNC2LI1
NM_016008.4 intron
NM_016008.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.57
Genes affected
DYNC2LI1 (HGNC:24595): (dynein cytoplasmic 2 light intermediate chain 1) This gene encodes a protein that is a component of the dynein-2 microtubule motor protein complex that plays a role in the retrograde transport of cargo in primary cilia via the intraflagellar transport system. This gene is ubiquitously expressed and its protein, which localizes to the axoneme and Golgi apparatus, interacts directly with the cytoplasmic dynein 2 heavy chain 1 protein to form part of the multi-protein dynein-2 complex. Mutations in this gene produce defects in the dynein-2 complex which result in several types of ciliopathy including short-rib thoracic dysplasia 15 with polydactyly (SRTD15). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-43800829-AT-A is Pathogenic according to our data. Variant chr2-43800829-AT-A is described in ClinVar as [Pathogenic]. Clinvar id is 518440.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYNC2LI1 | NM_016008.4 | c.655-9delT | intron_variant | ENST00000260605.12 | NP_057092.2 | |||
DYNC2LI1 | NM_001348913.2 | c.658-9delT | intron_variant | NP_001335842.1 | ||||
DYNC2LI1 | NM_001348912.2 | c.655-9delT | intron_variant | NP_001335841.1 | ||||
DYNC2LI1 | NM_001193464.2 | c.658-9delT | intron_variant | NP_001180393.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNC2LI1 | ENST00000260605.12 | c.655-9delT | intron_variant | 1 | NM_016008.4 | ENSP00000260605.8 | ||||
DYNC2LI1 | ENST00000605786.5 | c.658-9delT | intron_variant | 1 | ENSP00000474032.1 | |||||
DYNC2LI1 | ENST00000378587.3 | c.604-9delT | intron_variant | 1 | ENSP00000367850.3 | |||||
DYNC2LI1 | ENST00000489222.6 | n.611-9delT | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152026Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000132 AC: 3AN: 228054Hom.: 0 AF XY: 0.00000806 AC XY: 1AN XY: 124062
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GnomAD4 exome AF: 0.0000200 AC: 27AN: 1348582Hom.: 0 Cov.: 20 AF XY: 0.0000193 AC XY: 13AN XY: 675278
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74248
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Short-rib thoracic dysplasia 15 with polydactyly Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 17, 2023 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 12
Find out detailed SpliceAI scores and Pangolin per-transcript scores at