rs2071201
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000444.6(PHEX):c.119-455C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 110,269 control chromosomes in the GnomAD database, including 2,561 homozygotes. There are 7,012 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHEX | NM_000444.6 | c.119-455C>T | intron_variant | ENST00000379374.5 | NP_000435.3 | |||
PHEX | NM_001282754.2 | c.119-455C>T | intron_variant | NP_001269683.1 | ||||
PHEX | XM_047442159.1 | c.119-455C>T | intron_variant | XP_047298115.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHEX | ENST00000379374.5 | c.119-455C>T | intron_variant | 1 | NM_000444.6 | ENSP00000368682.4 | ||||
PHEX | ENST00000684143.1 | c.119-455C>T | intron_variant | ENSP00000508264.1 | ||||||
PHEX | ENST00000475778.2 | n.545-455C>T | intron_variant | 5 | ||||||
PHEX | ENST00000683214.1 | n.544+4891C>T | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.231 AC: 25486AN: 110213Hom.: 2557 Cov.: 22 AF XY: 0.215 AC XY: 6990AN XY: 32497
GnomAD4 genome AF: 0.231 AC: 25520AN: 110269Hom.: 2561 Cov.: 22 AF XY: 0.215 AC XY: 7012AN XY: 32563
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at