rs113364886
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_153240.5(NPHP3):c.3971T>C(p.Phe1324Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,614,144 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_153240.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.3971T>C | p.Phe1324Ser | missense_variant | 27/27 | ENST00000337331.10 | |
NPHP3-ACAD11 | NR_037804.1 | n.3977T>C | non_coding_transcript_exon_variant | 26/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.3971T>C | p.Phe1324Ser | missense_variant | 27/27 | 1 | NM_153240.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00118 AC: 180AN: 152240Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000310 AC: 78AN: 251382Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135868
GnomAD4 exome AF: 0.000198 AC: 290AN: 1461786Hom.: 3 Cov.: 30 AF XY: 0.000186 AC XY: 135AN XY: 727198
GnomAD4 genome ? AF: 0.00119 AC: 182AN: 152358Hom.: 1 Cov.: 32 AF XY: 0.00110 AC XY: 82AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 06, 2017 | - - |
Kidney disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Feb 06, 2017 | - - |
Nephronophthisis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 27, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at