rs149894086
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_022356.4(P3H1):āc.1529A>Gā(p.Asn510Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,614,108 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. N510T) has been classified as Uncertain significance.
Frequency
Consequence
NM_022356.4 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 |
---|---|---|---|---|---|---|---|
P3H1 | NM_022356.4 | c.1529A>G | p.Asn510Ser | missense_variant | 10/15 | ENST00000296388.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P3H1 | ENST00000296388.10 | c.1529A>G | p.Asn510Ser | missense_variant | 10/15 | 1 | NM_022356.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000894 AC: 136AN: 152148Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251472Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135914
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461842Hom.: 1 Cov.: 32 AF XY: 0.0000866 AC XY: 63AN XY: 727230
GnomAD4 genome AF: 0.000893 AC: 136AN: 152266Hom.: 1 Cov.: 32 AF XY: 0.000859 AC XY: 64AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 12, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 24, 2016 | - - |
Osteogenesis imperfecta type 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
P3H1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 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