17-28912578-T-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001033561.2(PHF12):āc.1993A>Gā(p.Asn665Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000052 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00024 ( 0 hom., cov: 32)
Exomes š: 0.000032 ( 0 hom. )
Consequence
PHF12
NM_001033561.2 missense
NM_001033561.2 missense
Scores
5
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.78
Genes affected
PHF12 (HGNC:20816): (PHD finger protein 12) Enables phosphatidylinositol binding activity and transcription corepressor activity. Involved in negative regulation of transcription, DNA-templated. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of Sin3 complex and transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.022037268).
BS2
High AC in GnomAd4 at 37 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF12 | NM_001033561.2 | c.1993A>G | p.Asn665Asp | missense_variant | 9/15 | ENST00000332830.9 | |
PHF12 | NM_001290131.2 | c.1993A>G | p.Asn665Asp | missense_variant | 9/11 | ||
PHF12 | NM_020889.3 | c.1993A>G | p.Asn665Asp | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF12 | ENST00000332830.9 | c.1993A>G | p.Asn665Asp | missense_variant | 9/15 | 2 | NM_001033561.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000103 AC: 26AN: 251454Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135902
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GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727246
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GnomAD4 genome AF: 0.000243 AC: 37AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74450
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;L;.;L
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.;.;N
REVEL
Uncertain
Sift
Benign
T;.;.;D
Sift4G
Benign
T;T;.;T
Polyphen
B;.;.;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at