chr3-132681258-C-CT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_153240.5(NPHP3):c.*651_*652insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 105,608 control chromosomes in the GnomAD database, including 49 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 49 hom., cov: 23)
Exomes 𝑓: 0.027 ( 0 hom. )
Consequence
NPHP3
NM_153240.5 3_prime_UTR
NM_153240.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.19
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 3-132681258-C-CT is Benign according to our data. Variant chr3-132681258-C-CT is described in ClinVar as [Benign]. Clinvar id is 1264737.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.*651_*652insA | 3_prime_UTR_variant | 27/27 | ENST00000337331.10 | NP_694972.3 | ||
NPHP3-ACAD11 | NR_037804.1 | n.3995+655_3995+656insA | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.*651_*652insA | 3_prime_UTR_variant | 27/27 | 1 | NM_153240.5 | ENSP00000338766 | P1 | ||
NPHP3 | ENST00000474871.5 | n.3843_3844insA | non_coding_transcript_exon_variant | 11/11 | 2 | |||||
NPHP3 | ENST00000493732.5 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0238 AC: 2512AN: 105526Hom.: 48 Cov.: 23
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GnomAD4 exome AF: 0.0270 AC: 2AN: 74Hom.: 0 Cov.: 0 AF XY: 0.0370 AC XY: 2AN XY: 54
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GnomAD4 genome AF: 0.0238 AC: 2512AN: 105534Hom.: 49 Cov.: 23 AF XY: 0.0219 AC XY: 1076AN XY: 49058
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 04, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at