6-33415085-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024165.3(PHF1):c.1180C>T(p.Arg394Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,612,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024165.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000935 AC: 23AN: 245990Hom.: 0 AF XY: 0.000113 AC XY: 15AN XY: 133188
GnomAD4 exome AF: 0.000202 AC: 295AN: 1460558Hom.: 0 Cov.: 38 AF XY: 0.000198 AC XY: 144AN XY: 726520
GnomAD4 genome AF: 0.0000987 AC: 15AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1180C>T (p.R394C) alteration is located in exon 12 (coding exon 11) of the PHF1 gene. This alteration results from a C to T substitution at nucleotide position 1180, causing the arginine (R) at amino acid position 394 to be replaced by a cysteine (C). 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