rs755145737
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004426.3(PHC1):c.2627G>A(p.Arg876Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000368 in 1,603,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R876W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004426.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHC1 | NM_004426.3 | c.2627G>A | p.Arg876Gln | missense_variant, splice_region_variant | 13/15 | ENST00000544916.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHC1 | ENST00000544916.6 | c.2627G>A | p.Arg876Gln | missense_variant, splice_region_variant | 13/15 | 1 | NM_004426.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000168 AC: 4AN: 237554Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128928
GnomAD4 exome AF: 0.0000338 AC: 49AN: 1451052Hom.: 0 Cov.: 31 AF XY: 0.0000347 AC XY: 25AN XY: 721380
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 20, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at