rs779336075
Positions:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015102.5(NPHP4):c.3123C>T(p.Phe1041=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,458,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
NPHP4
NM_015102.5 synonymous
NM_015102.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.98
Genes affected
NPHP4 (HGNC:19104): (nephrocystin 4) This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 1-5874579-G-A is Benign according to our data. Variant chr1-5874579-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 413603.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.98 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHP4 | NM_015102.5 | c.3123C>T | p.Phe1041= | synonymous_variant | 22/30 | ENST00000378156.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHP4 | ENST00000378156.9 | c.3123C>T | p.Phe1041= | synonymous_variant | 22/30 | 1 | NM_015102.5 | P2 | |
NPHP4 | ENST00000378169.7 | c.*2024C>T | 3_prime_UTR_variant, NMD_transcript_variant | 19/27 | 1 | ||||
NPHP4 | ENST00000478423.6 | n.2855C>T | non_coding_transcript_exon_variant | 18/26 | 2 | ||||
NPHP4 | ENST00000489180.6 | c.*934C>T | 3_prime_UTR_variant, NMD_transcript_variant | 25/33 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241758Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131530
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GnomAD4 exome AF: 0.00000412 AC: 6AN: 1458018Hom.: 0 Cov.: 34 AF XY: 0.00000552 AC XY: 4AN XY: 724880
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Nephronophthisis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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