rs201302396
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001080463.2(DYNC2H1):c.5088G>A(p.Thr1696=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,612,080 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 1 hom. )
Consequence
DYNC2H1
NM_001080463.2 synonymous
NM_001080463.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.73
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 11-103170227-G-A is Benign according to our data. Variant chr11-103170227-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 528905.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.73 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.5088G>A | p.Thr1696= | synonymous_variant | 33/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.5088G>A | p.Thr1696= | synonymous_variant | 33/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.5088G>A | p.Thr1696= | synonymous_variant | 33/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.5088G>A | p.Thr1696= | synonymous_variant | 33/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2205+35808G>A | intron_variant | 1 | |||||
DYNC2H1 | ENST00000649323.1 | c.*2633G>A | 3_prime_UTR_variant, NMD_transcript_variant | 31/51 |
Frequencies
GnomAD3 genomes ? AF: 0.000657 AC: 100AN: 152144Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000142 AC: 35AN: 246342Hom.: 0 AF XY: 0.000135 AC XY: 18AN XY: 133614
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GnomAD4 exome AF: 0.000110 AC: 161AN: 1459818Hom.: 1 Cov.: 30 AF XY: 0.000113 AC XY: 82AN XY: 726076
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GnomAD4 genome ? AF: 0.000657 AC: 100AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74434
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Jeune thoracic dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational 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