rs12294076
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001080463.2(DYNC2H1):c.10482+96T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,250,336 control chromosomes in the GnomAD database, including 1,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.064 ( 1058 hom., cov: 32)
Exomes 𝑓: 0.0061 ( 701 hom. )
Consequence
DYNC2H1
NM_001080463.2 intron
NM_001080463.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0120
Genes affected
DYNC2H1 (HGNC:2962): (dynein cytoplasmic 2 heavy chain 1) This gene encodes a large cytoplasmic dynein protein that is involved in retrograde transport in the cilium and has a role in intraflagellar transport, a process required for ciliary/flagellar assembly. Mutations in this gene cause a heterogeneous spectrum of conditions related to altered primary cilium function and often involve polydactyly, abnormal skeletogenesis, and polycystic kidneys. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 11-103256336-T-C is Benign according to our data. Variant chr11-103256336-T-C is described in ClinVar as [Benign]. Clinvar id is 1271829.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.10482+96T>C | intron_variant | ENST00000650373.2 | |||
DYNC2H1 | NM_001377.3 | c.10461+96T>C | intron_variant | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000375735.7 | c.10461+96T>C | intron_variant | 1 | NM_001377.3 | P3 | |||
DYNC2H1 | ENST00000650373.2 | c.10482+96T>C | intron_variant | NM_001080463.2 | A1 | ||||
DYNC2H1 | ENST00000334267.11 | c.2205+121917T>C | intron_variant | 1 | |||||
ENST00000649070.1 | n.691-4032A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0638 AC: 9709AN: 152072Hom.: 1054 Cov.: 32
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GnomAD4 exome AF: 0.00609 AC: 6688AN: 1098146Hom.: 701 AF XY: 0.00534 AC XY: 2942AN XY: 551116
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GnomAD4 genome ? AF: 0.0639 AC: 9729AN: 152190Hom.: 1058 Cov.: 32 AF XY: 0.0607 AC XY: 4517AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
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