rs886058000
Your query was ambiguous. Multiple possible variants found:
- chr3-132681258-CTTTTTTTTTTTTT-C
- chr3-132681258-CTTTTTTTTTTTTT-CT
- chr3-132681258-CTTTTTTTTTTTTT-CTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTT
- chr3-132681258-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_153240.5(NPHP3):c.*639_*651delAAAAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000189 in 105,586 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 0.000019 ( 0 hom., cov: 23)
Consequence
NPHP3
NM_153240.5 3_prime_UTR
NM_153240.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.19
Publications
0 publications found
Genes affected
NPHP3 (HGNC:7907): (nephrocystin 3) This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]
NPHP3-ACAD11 (HGNC:48351): (NPHP3-ACAD11 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring NPHP3 (nephronophthisis 3, adolescent) and ACAD11 (acyl-CoA dehydrogenase family, member 11) genes on chromosome 3. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
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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_153240.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| NPHP3 | NM_153240.5 | MANE Select | c.*639_*651delAAAAAAAAAAAAA | 3_prime_UTR | Exon 27 of 27 | NP_694972.3 | |||
| NPHP3-ACAD11 | NR_037804.1 | n.3995+643_3995+655delAAAAAAAAAAAAA | intron | N/A |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NPHP3 | ENST00000337331.10 | TSL:1 MANE Select | c.*639_*651delAAAAAAAAAAAAA | 3_prime_UTR | Exon 27 of 27 | ENSP00000338766.5 | Q7Z494-1 | ||
| NPHP3-ACAD11 | ENST00000632629.1 | TSL:2 | c.635+643_635+655delAAAAAAAAAAAAA | intron | N/A | ENSP00000488520.1 | A0A0J9YXS1 | ||
| NPHP3 | ENST00000971413.1 | c.*639_*651delAAAAAAAAAAAAA | splice_region | Exon 25 of 25 | ENSP00000641472.1 |
Frequencies
GnomAD3 genomes 0.0000189 AC: 2AN: 105586Hom.: 0 Cov.: 23 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
105586
Hom.:
Cov.:
23
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 0.0000189 AC: 2AN: 105586Hom.: 0 Cov.: 23 AF XY: 0.0000204 AC XY: 1AN XY: 49086 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
105586
Hom.:
Cov.:
23
AF XY:
AC XY:
1
AN XY:
49086
show subpopulations
African (AFR)
AF:
AC:
0
AN:
27610
American (AMR)
AF:
AC:
0
AN:
10190
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2788
East Asian (EAS)
AF:
AC:
0
AN:
2720
South Asian (SAS)
AF:
AC:
0
AN:
2984
European-Finnish (FIN)
AF:
AC:
1
AN:
4196
Middle Eastern (MID)
AF:
AC:
0
AN:
194
European-Non Finnish (NFE)
AF:
AC:
0
AN:
52810
Other (OTH)
AF:
AC:
1
AN:
1420
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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
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