14-66508553-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_020806.5(GPHN):āc.26C>Gā(p.Thr9Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00107 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T9A) has been classified as Uncertain significance.
Frequency
Consequence
NM_020806.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPHN | NM_020806.5 | c.26C>G | p.Thr9Ser | missense_variant | 1/23 | ENST00000478722.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPHN | ENST00000478722.6 | c.26C>G | p.Thr9Ser | missense_variant | 1/23 | 1 | NM_020806.5 |
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 162AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00136 AC: 342AN: 251468Hom.: 2 AF XY: 0.00148 AC XY: 201AN XY: 135914
GnomAD4 exome AF: 0.00108 AC: 1572AN: 1461764Hom.: 1 Cov.: 30 AF XY: 0.00116 AC XY: 842AN XY: 727194
GnomAD4 genome AF: 0.00106 AC: 162AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.00113 AC XY: 84AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | GPHN: BS1, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type A Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Jul 27, 2016 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
GPHN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 20, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at