chrX-53940207-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_015107.3(PHF8):c.2959G>A(p.Gly987Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,184,263 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015107.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF8 | NM_015107.3 | c.2959G>A | p.Gly987Ser | missense_variant | 21/22 | ENST00000338154.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF8 | ENST00000338154.11 | c.2959G>A | p.Gly987Ser | missense_variant | 21/22 | 1 | NM_015107.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111894Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34088
GnomAD4 exome AF: 0.00000933 AC: 10AN: 1072369Hom.: 0 Cov.: 31 AF XY: 0.00000860 AC XY: 3AN XY: 348931
GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111894Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34088
ClinVar
Submissions by phenotype
Syndromic X-linked intellectual disability Siderius type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at