rs11279953
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-A
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
- chr15-43370975-ACCCCGGCCCCGGCCCCGG-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001372080.1(ZSCAN29):c.-548_-531delCCGGGGCCGGGGCCGGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 259,450 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000092 ( 0 hom. )
Consequence
ZSCAN29
NM_001372080.1 5_prime_UTR
NM_001372080.1 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.691
Publications
0 publications found
Genes affected
ZSCAN29 (HGNC:26673): (zinc finger and SCAN domain containing 29) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
TUBGCP4 (HGNC:16691): (tubulin gamma complex component 4) This gene encodes a component of the gamma-tubulin ring complex, which is required for microtubule nucleation. In mammalian cells, the protein localizes to centrosomes in association with gamma-tubulin. Crystal structure analysis revealed a structure composed of five helical bundles arranged around conserved hydrophobic cores. An exposed surface area located in the C-terminal domain is essential and sufficient for direct binding to gamma-tubulin. Mutations in this gene that alter microtubule organization are associated with microcephaly and chorioretinopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]
TUBGCP4 Gene-Disease associations (from GenCC):
- microcephaly and chorioretinopathy 3Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- microcephaly and chorioretinopathy 1Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001372080.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZSCAN29 | NM_001372080.1 | MANE Select | c.-548_-531delCCGGGGCCGGGGCCGGGG | 5_prime_UTR | Exon 1 of 6 | NP_001359009.1 | Q8IWY8-1 | ||
| TUBGCP4 | NM_014444.5 | MANE Select | c.-379_-362delCCCCGGCCCCGGCCCCGG | upstream_gene | N/A | NP_055259.2 | |||
| TUBGCP4 | NM_001286414.3 | c.-379_-362delCCCCGGCCCCGGCCCCGG | upstream_gene | N/A | NP_001273343.1 | Q9UGJ1-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZSCAN29 | ENST00000684362.1 | MANE Select | c.-548_-531delCCGGGGCCGGGGCCGGGG | 5_prime_UTR | Exon 1 of 6 | ENSP00000507363.1 | Q8IWY8-1 | ||
| ZSCAN29 | ENST00000942835.1 | c.-548_-531delCCGGGGCCGGGGCCGGGG | 5_prime_UTR | Exon 1 of 6 | ENSP00000612894.1 | ||||
| ZSCAN29 | ENST00000923737.1 | c.-544_-527delCCGGGGCCGGGGCCGGGG | 5_prime_UTR | Exon 1 of 6 | ENSP00000593796.1 |
Frequencies
GnomAD3 genomes 0.000193 AC: 29AN: 150448Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
29
AN:
150448
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000918 AC: 10AN: 108886Hom.: 0 AF XY: 0.0000851 AC XY: 5AN XY: 58760 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
108886
Hom.:
AF XY:
AC XY:
5
AN XY:
58760
show subpopulations
African (AFR)
AF:
AC:
7
AN:
3246
American (AMR)
AF:
AC:
0
AN:
5356
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2620
East Asian (EAS)
AF:
AC:
1
AN:
4850
South Asian (SAS)
AF:
AC:
2
AN:
18546
European-Finnish (FIN)
AF:
AC:
0
AN:
5592
Middle Eastern (MID)
AF:
AC:
0
AN:
442
European-Non Finnish (NFE)
AF:
AC:
0
AN:
62238
Other (OTH)
AF:
AC:
0
AN:
5996
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.000193 AC: 29AN: 150564Hom.: 0 Cov.: 0 AF XY: 0.000231 AC XY: 17AN XY: 73446 show subpopulations
GnomAD4 genome
AF:
AC:
29
AN:
150564
Hom.:
Cov.:
0
AF XY:
AC XY:
17
AN XY:
73446
show subpopulations
African (AFR)
AF:
AC:
27
AN:
41234
American (AMR)
AF:
AC:
0
AN:
15192
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3462
East Asian (EAS)
AF:
AC:
0
AN:
4968
South Asian (SAS)
AF:
AC:
1
AN:
4720
European-Finnish (FIN)
AF:
AC:
1
AN:
10382
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67338
Other (OTH)
AF:
AC:
0
AN:
2084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.516
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.