6-63684334-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001370348.2(PHF3):c.612C>T(p.Ser204Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,613,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001370348.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF3 | NM_001370348.2 | c.612C>T | p.Ser204Ser | synonymous_variant | Exon 4 of 16 | ENST00000262043.8 | NP_001357277.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000914 AC: 139AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000299 AC: 75AN: 251120Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135714
GnomAD4 exome AF: 0.000125 AC: 182AN: 1461632Hom.: 0 Cov.: 33 AF XY: 0.0000963 AC XY: 70AN XY: 727116
GnomAD4 genome AF: 0.000920 AC: 140AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000994 AC XY: 74AN XY: 74442
ClinVar
Submissions by phenotype
PHF3-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at