9-93649079-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005392.4(PHF2):c.469C>T(p.Arg157Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,399,284 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_005392.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHF2 | ENST00000359246.9 | c.469C>T | p.Arg157Trp | missense_variant | Exon 5 of 22 | 1 | NM_005392.4 | ENSP00000352185.4 | ||
PHF2 | ENST00000610682.1 | c.239+12614C>T | intron_variant | Intron 3 of 7 | 5 | ENSP00000479936.1 | ||||
PHF2 | ENST00000375376.8 | c.187-4188C>T | intron_variant | Intron 3 of 8 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000929 AC: 13AN: 1399284Hom.: 0 Cov.: 32 AF XY: 0.00000869 AC XY: 6AN XY: 690156
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.469C>T (p.R157W) alteration is located in exon 5 (coding exon 5) of the PHF2 gene. This alteration results from a C to T substitution at nucleotide position 469, causing the arginine (R) at amino acid position 157 to be replaced by a tryptophan (W). 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