X-134393948-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The ENST00000370803.8(PHF6):c.414C>T(p.Ser138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000522 in 1,207,879 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 31 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
ENST00000370803.8 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF6 | NM_001015877.2 | c.414C>T | p.Ser138= | synonymous_variant | 5/11 | ENST00000370803.8 | NP_001015877.1 | |
PHF6 | NM_032458.3 | c.414C>T | p.Ser138= | synonymous_variant | 5/10 | NP_115834.1 | ||
PHF6 | NM_032335.3 | c.414C>T | p.Ser138= | synonymous_variant | 5/8 | NP_115711.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHF6 | ENST00000370803.8 | c.414C>T | p.Ser138= | synonymous_variant | 5/11 | 1 | NM_001015877.2 | ENSP00000359839 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000108 AC: 12AN: 111045Hom.: 0 Cov.: 23 AF XY: 0.000150 AC XY: 5AN XY: 33297
GnomAD3 exomes AF: 0.000115 AC: 21AN: 183178Hom.: 0 AF XY: 0.000148 AC XY: 10AN XY: 67690
GnomAD4 exome AF: 0.0000465 AC: 51AN: 1096788Hom.: 0 Cov.: 29 AF XY: 0.0000718 AC XY: 26AN XY: 362230
GnomAD4 genome AF: 0.000108 AC: 12AN: 111091Hom.: 0 Cov.: 23 AF XY: 0.000150 AC XY: 5AN XY: 33353
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 18, 2016 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 04, 2015 | - - |
PHF6-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Borjeson-Forssman-Lehmann syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at