6-63684220-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001370348.2(PHF3):āc.498A>Gā(p.Val166Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00154 in 1,614,050 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001370348.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF3 | NM_001370348.2 | c.498A>G | p.Val166Val | synonymous_variant | Exon 4 of 16 | ENST00000262043.8 | NP_001357277.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00771 AC: 1173AN: 152192Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00208 AC: 522AN: 251348Hom.: 8 AF XY: 0.00165 AC XY: 224AN XY: 135844
GnomAD4 exome AF: 0.000896 AC: 1309AN: 1461740Hom.: 17 Cov.: 33 AF XY: 0.000815 AC XY: 593AN XY: 727162
GnomAD4 genome AF: 0.00771 AC: 1175AN: 152310Hom.: 12 Cov.: 32 AF XY: 0.00722 AC XY: 538AN XY: 74498
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