6-63680067-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370350.2(PHF3):c.-99A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,612,784 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 Uncertain significance (★).
Frequency
Consequence
NM_001370350.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF3 | NM_001370348.2 | c.312A>T | p.Glu104Asp | missense_variant | Exon 3 of 16 | ENST00000262043.8 | NP_001357277.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250856Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135610
GnomAD4 exome AF: 0.000120 AC: 176AN: 1460660Hom.: 0 Cov.: 30 AF XY: 0.000117 AC XY: 85AN XY: 726656
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.312A>T (p.E104D) alteration is located in exon 2 (coding exon 2) of the PHF3 gene. This alteration results from a A to T substitution at nucleotide position 312, causing the glutamic acid (E) at amino acid position 104 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at