chr3-132684624-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_153240.5(NPHP3):c.3500G>A(p.Arg1167His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000316 in 1,613,974 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1167C) has been classified as Uncertain significance.
Frequency
Consequence
NM_153240.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.3500G>A | p.Arg1167His | missense_variant | 24/27 | ENST00000337331.10 | |
NPHP3-ACAD11 | NR_037804.1 | n.3506G>A | non_coding_transcript_exon_variant | 23/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.3500G>A | p.Arg1167His | missense_variant | 24/27 | 1 | NM_153240.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 152166Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000334 AC: 84AN: 251206Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135794
GnomAD4 exome AF: 0.000220 AC: 321AN: 1461690Hom.: 3 Cov.: 31 AF XY: 0.000206 AC XY: 150AN XY: 727138
GnomAD4 genome AF: 0.00124 AC: 189AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.00113 AC XY: 84AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 06, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Kidney disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Apr 17, 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 | May 01, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at