6-63684419-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001370348.2(PHF3):c.697G>A(p.Gly233Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00133 in 1,613,986 control chromosomes in the GnomAD database, including 27 homozygotes. 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 Benign (no stars).
Frequency
Consequence
NM_001370348.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF3 | NM_001370348.2 | c.697G>A | p.Gly233Arg | missense_variant | Exon 4 of 16 | ENST00000262043.8 | NP_001357277.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00659 AC: 1003AN: 152142Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00185 AC: 465AN: 251262Hom.: 6 AF XY: 0.00147 AC XY: 199AN XY: 135798
GnomAD4 exome AF: 0.000781 AC: 1142AN: 1461726Hom.: 16 Cov.: 32 AF XY: 0.000710 AC XY: 516AN XY: 727166
GnomAD4 genome AF: 0.00660 AC: 1005AN: 152260Hom.: 11 Cov.: 32 AF XY: 0.00622 AC XY: 463AN XY: 74436
ClinVar
Submissions by phenotype
PHF3-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at