rs72253125
Your query was ambiguous. Multiple possible variants found:
- chr11-94129088-TCCCGCCCCGCCCCGC-T
- chr11-94129088-TCCCGCCCCGCCCCGC-TCCCGC
- chr11-94129088-TCCCGCCCCGCCCCGC-TCCCGCCCCGC
- chr11-94129088-TCCCGCCCCGCCCCGC-TCCCGCCCCGCCCCGCCCCGC
- chr11-94129088-TCCCGCCCCGCCCCGC-TCCCGCCCCGCCCCGCCCCGCCCCGC
- chr11-94129088-TCCCGCCCCGCCCCGC-TCCCGCCCCGCCCCGCCCCGCCCCGCCCCGC
- chr11-94129088-TCCCGCCCCGCCCCGC-TCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_015368.4(PANX1):c.-218_-204delCCGCCCCGCCCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.000013 ( 0 hom., cov: 0)
Consequence
PANX1
NM_015368.4 5_prime_UTR
NM_015368.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.929
Publications
1 publications found
Genes affected
PANX1 (HGNC:8599): (pannexin 1) The protein encoded by this gene belongs to the innexin family. Innexin family members are the structural components of gap junctions. This protein and pannexin 2 are abundantly expressed in central nerve system (CNS) and are coexpressed in various neuronal populations. Studies in Xenopus oocytes suggest that this protein alone and in combination with pannexin 2 may form cell type-specific gap junctions with distinct properties. [provided by RefSeq, Jul 2008]
PANX1 Gene-Disease associations (from GenCC):
- oocyte maturation defect 7Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PANX1 | NM_015368.4 | c.-218_-204delCCGCCCCGCCCCGCC | 5_prime_UTR_variant | Exon 1 of 5 | ENST00000227638.8 | NP_056183.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PANX1 | ENST00000227638.8 | c.-218_-204delCCGCCCCGCCCCGCC | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_015368.4 | ENSP00000227638.3 | |||
| PANX1 | ENST00000436171.2 | c.-218_-204delCCGCCCCGCCCCGCC | 5_prime_UTR_variant | Exon 1 of 5 | 1 | ENSP00000411461.2 |
Frequencies
GnomAD3 genomes 0.0000134 AC: 2AN: 149800Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
149800
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000133 AC: 2AN: 149902Hom.: 0 Cov.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 73100 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
2
AN:
149902
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
73100
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
40980
American (AMR)
AF:
AC:
0
AN:
15170
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3446
East Asian (EAS)
AF:
AC:
0
AN:
4900
South Asian (SAS)
AF:
AC:
2
AN:
4734
European-Finnish (FIN)
AF:
AC:
0
AN:
10370
Middle Eastern (MID)
AF:
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67056
Other (OTH)
AF:
AC:
0
AN:
2078
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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
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