rs373261521
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_000444.6(PHEX):c.957G>A(p.Lys319=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,206,943 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 77 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000444.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHEX | NM_000444.6 | c.957G>A | p.Lys319= | synonymous_variant | 9/22 | ENST00000379374.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHEX | ENST00000379374.5 | c.957G>A | p.Lys319= | synonymous_variant | 9/22 | 1 | NM_000444.6 | P1 | |
PHEX | ENST00000684143.1 | c.954G>A | p.Lys318= | synonymous_variant | 9/11 | ||||
PHEX | ENST00000475778.2 | n.1383G>A | non_coding_transcript_exon_variant | 9/9 | 5 | ||||
PHEX | ENST00000684745.1 | n.631G>A | non_coding_transcript_exon_variant | 7/20 |
Frequencies
GnomAD3 genomes ? AF: 0.000109 AC: 12AN: 110382Hom.: 0 Cov.: 22 AF XY: 0.0000307 AC XY: 1AN XY: 32620
GnomAD3 exomes AF: 0.0000765 AC: 14AN: 183098Hom.: 0 AF XY: 0.0000888 AC XY: 6AN XY: 67604
GnomAD4 exome AF: 0.000192 AC: 211AN: 1096561Hom.: 0 Cov.: 29 AF XY: 0.000210 AC XY: 76AN XY: 361965
GnomAD4 genome ? AF: 0.000109 AC: 12AN: 110382Hom.: 0 Cov.: 22 AF XY: 0.0000307 AC XY: 1AN XY: 32620
ClinVar
Submissions by phenotype
Familial X-linked hypophosphatemic vitamin D refractory rickets Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 01, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at