rs112199174
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_001015877.2(PHF6):c.927C>T(p.Asp309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,208,241 control chromosomes in the GnomAD database, including 14 homozygotes. There are 459 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_001015877.2 synonymous
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 |
---|---|---|---|---|---|---|---|
PHF6 | NM_001015877.2 | c.927C>T | p.Asp309= | synonymous_variant | 9/11 | ENST00000370803.8 | |
PHF6 | NM_032458.3 | c.927C>T | p.Asp309= | synonymous_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF6 | ENST00000370803.8 | c.927C>T | p.Asp309= | synonymous_variant | 9/11 | 1 | NM_001015877.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00740 AC: 829AN: 112046Hom.: 5 Cov.: 22 AF XY: 0.00624 AC XY: 214AN XY: 34288
GnomAD3 exomes AF: 0.00224 AC: 410AN: 183117Hom.: 5 AF XY: 0.00120 AC XY: 81AN XY: 67641
GnomAD4 exome AF: 0.000851 AC: 933AN: 1096140Hom.: 9 Cov.: 29 AF XY: 0.000669 AC XY: 242AN XY: 361730
GnomAD4 genome AF: 0.00742 AC: 832AN: 112101Hom.: 5 Cov.: 22 AF XY: 0.00632 AC XY: 217AN XY: 34353
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 14, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
PHF6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Borjeson-Forssman-Lehmann syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at