17-49224342-C-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_178500.4(PHOSPHO1):c.708G>T(p.Gln236His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,578,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 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
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHOSPHO1 | ENST00000310544.9 | c.708G>T | p.Gln236His | missense_variant | Exon 3 of 3 | 2 | NM_178500.4 | ENSP00000311925.4 | ||
PHOSPHO1 | ENST00000514112.1 | c.783G>T | p.Gln261His | missense_variant | Exon 2 of 2 | 1 | ENSP00000427694.1 | |||
PHOSPHO1 | ENST00000413580.5 | c.783G>T | p.Gln261His | missense_variant | Exon 3 of 3 | 2 | ENSP00000406909.1 | |||
PHOSPHO1 | ENST00000511066.5 | c.*97G>T | downstream_gene_variant | 2 | ENSP00000426095.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152256Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000614 AC: 11AN: 179232 AF XY: 0.0000606 show subpopulations
GnomAD4 exome AF: 0.000123 AC: 176AN: 1425762Hom.: 0 Cov.: 31 AF XY: 0.000106 AC XY: 75AN XY: 707304 show subpopulations
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74384 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.783G>T (p.Q261H) 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 783, causing the glutamine (Q) at amino acid position 261 to be replaced by a histidine (H). 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