chr3-50343122-CCA-C
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_015896.4(ZMYND10):c.593_594delTG(p.Val198GlyfsTer13) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000131 in 152,234 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Consequence
ZMYND10
NM_015896.4 frameshift
NM_015896.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.94
Publications
1 publications found
Genes affected
ZMYND10 (HGNC:19412): (zinc finger MYND-type containing 10) This gene encodes a protein containing a MYND-type zinc finger domain that likely functions in assembly of the dynein motor. Mutations in this gene can cause primary ciliary dyskinesia. This gene is also considered a tumor suppressor gene and is often mutated, deleted, or hypermethylated and silenced in cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-50343122-CCA-C is Pathogenic according to our data. Variant chr3-50343122-CCA-C is described in ClinVar as [Pathogenic]. Clinvar id is 66025.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZMYND10 | NM_015896.4 | c.593_594delTG | p.Val198GlyfsTer13 | frameshift_variant | Exon 6 of 12 | ENST00000231749.8 | NP_056980.2 | |
ZMYND10 | NM_001308379.2 | c.593_594delTG | p.Val198GlyfsTer71 | frameshift_variant | Exon 6 of 11 | NP_001295308.1 | ||
ZMYND10 | XM_005265216.4 | c.356_357delTG | p.Val119GlyfsTer13 | frameshift_variant | Exon 5 of 11 | XP_005265273.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152234
Hom.:
Cov.:
33
Gnomad AFR
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GnomAD2 exomes AF: 0.00000796 AC: 2AN: 251258 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152234
Hom.:
Cov.:
33
AF XY:
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0
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41462
American (AMR)
AF:
AC:
0
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
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0
AN:
5200
South Asian (SAS)
AF:
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0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10624
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68034
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
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Allele balance
Age Distribution
Genome Het
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 22 Pathogenic:1
Aug 08, 2013
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
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Computational scores
Source:
Name
Calibrated prediction
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Prediction
PhyloP100
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
Publications
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