rs763608782
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000444.6(PHEX):c.663+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000087 in 1,161,334 control chromosomes in the GnomAD database, including 1 homozygotes. There are 55 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000444.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHEX | NM_000444.6 | c.663+8G>A | splice_region_variant, intron_variant | ENST00000379374.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHEX | ENST00000379374.5 | c.663+8G>A | splice_region_variant, intron_variant | 1 | NM_000444.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000267 AC: 3AN: 112184Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34326
GnomAD3 exomes AF: 0.000186 AC: 34AN: 182434Hom.: 0 AF XY: 0.000282 AC XY: 19AN XY: 67264
GnomAD4 exome AF: 0.0000934 AC: 98AN: 1049150Hom.: 1 Cov.: 26 AF XY: 0.000168 AC XY: 54AN XY: 321444
GnomAD4 genome ? AF: 0.0000267 AC: 3AN: 112184Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34326
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 12, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 21, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at