chr17-49224568-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_178500.4(PHOSPHO1):c.482G>T(p.Arg161Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 1,564,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178500.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHOSPHO1 | NM_178500.4 | c.482G>T | p.Arg161Leu | missense_variant | 3/3 | ENST00000310544.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHOSPHO1 | ENST00000310544.9 | c.482G>T | p.Arg161Leu | missense_variant | 3/3 | 2 | NM_178500.4 | P1 | |
PHOSPHO1 | ENST00000514112.1 | c.557G>T | p.Arg186Leu | missense_variant | 2/2 | 1 | |||
PHOSPHO1 | ENST00000413580.5 | c.557G>T | p.Arg186Leu | missense_variant | 3/3 | 2 | |||
PHOSPHO1 | ENST00000511066.5 | c.482G>T | p.Arg161Leu | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000585 AC: 1AN: 171046Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93786
GnomAD4 exome AF: 0.00000921 AC: 13AN: 1412254Hom.: 0 Cov.: 31 AF XY: 0.0000100 AC XY: 7AN XY: 699562
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2022 | The c.557G>T (p.R186L) alteration is located in exon 3 (coding exon 1) of the PHOSPHO1 gene. This alteration results from a G to T substitution at nucleotide position 557, causing the arginine (R) at amino acid position 186 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at