rs12559632
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000444.6(PHEX):c.1404+9251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 111,648 control chromosomes in the GnomAD database, including 2,777 homozygotes. There are 8,419 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000444.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHEX | NM_000444.6 | c.1404+9251G>A | intron_variant | ENST00000379374.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHEX | ENST00000379374.5 | c.1404+9251G>A | intron_variant | 1 | NM_000444.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.259 AC: 28863AN: 111594Hom.: 2769 Cov.: 23 AF XY: 0.249 AC XY: 8418AN XY: 33790
GnomAD4 genome ? AF: 0.259 AC: 28874AN: 111648Hom.: 2777 Cov.: 23 AF XY: 0.249 AC XY: 8419AN XY: 33854
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at