chr2-43774161-C-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_016008.4(DYNC2LI1):c.8+15C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,613,840 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0043 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 36 hom. )
Consequence
DYNC2LI1
NM_016008.4 intron
NM_016008.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.436
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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 2-43774161-C-G is Benign according to our data. Variant chr2-43774161-C-G is described in ClinVar as [Benign]. Clinvar id is 1642468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00433 (659/152318) while in subpopulation SAS AF= 0.0189 (91/4824). AF 95% confidence interval is 0.0157. There are 8 homozygotes in gnomad4. There are 329 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYNC2LI1 | NM_016008.4 | c.8+15C>G | intron_variant | ENST00000260605.12 | NP_057092.2 | |||
LOC105374571 | XR_940033.2 | n.9C>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNC2LI1 | ENST00000260605.12 | c.8+15C>G | intron_variant | 1 | NM_016008.4 | ENSP00000260605 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00426 AC: 649AN: 152200Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00303 AC: 757AN: 249918Hom.: 10 AF XY: 0.00339 AC XY: 459AN XY: 135294
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GnomAD4 exome AF: 0.00141 AC: 2067AN: 1461522Hom.: 36 Cov.: 30 AF XY: 0.00181 AC XY: 1316AN XY: 727028
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GnomAD4 genome AF: 0.00433 AC: 659AN: 152318Hom.: 8 Cov.: 32 AF XY: 0.00442 AC XY: 329AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at