Starting
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PHF6
Final classification
VUS
PHF6 c.823G>A · p.Gly275Arg
PHF6

NM_001015877.1:c.823G>A (p.Gly275Arg) in PHF6 is absent from gnomAD v2.1 and v4.1 population databases, supporting PM2.

Gene
PHF6
Transcript
NM_001015877.1
HGVS · transcript:coding
NM_001015877.1:c.823G>A
Consequence
N/A
GRCh38
chrX:134415109 G>A
GRCh37
chrX:133549139 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting; combination = 2 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
PHF6 c.823G>A

NM_001015877.1:c.823G>A (p.Gly275Arg) in PHF6 is absent from gnomAD v2.1 and v4.1 population databases, supporting PM2.1 Gly275 resides within the extended PHD finger domain 2 (ePHD2, residues 249-295), a functionally critical domain for PHF6 nucleolar localization and transcriptional regulation, supporting PM1 at supporting weight. The variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory, SCV001142206) with maternal origin; no de novo occurrence, pathogenic assertion, or functional evidence was identified.2 No pathogenic missense comparator at codon 275, no case-control data, no cosegregation data, and no functional studies were identified, leaving PS1, PS4, PS5, PP1, PS3, and PM5 unmet. In silico predictions are inconclusive: BayesDel score is borderline (0.4267), SpliceAI predicts no splice impact (max delta 0.01), and REVEL is unavailable, insufficient for PP3 or BP4.3 Applying generic ACMG/AMP 2015 final combination rules (PMID:25741868), two supporting pathogenic criteria (PM1_Supporting + PM2_Supporting) are insufficient to reach Likely Pathogenic; no benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM1 + PM2 VUS
3 bayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_001015877.1 · variants mapped to exon structure
PHF6 NM_001015877.1
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 804232)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). BayesDel score = 0.426665.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PHF6, a chromatin binding protein, is frequently altered by mutation and deletion in a range of hematologic malignancies.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV59699628, n = 3 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots