rs193921057
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_005392.4(PHF2):c.2563G>A(p.Asp855Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000262 in 1,612,122 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00025 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 1 hom. )
Consequence
PHF2
NM_005392.4 missense
NM_005392.4 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 7.63
Genes affected
PHF2 (HGNC:8920): (PHD finger protein 2) This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, PHF2
BP4
?
Computational evidence support a benign effect (MetaRNN=0.14442858).
BS2
?
High AC in GnomAd at 38 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF2 | NM_005392.4 | c.2563G>A | p.Asp855Asn | missense_variant | 18/22 | ENST00000359246.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF2 | ENST00000359246.9 | c.2563G>A | p.Asp855Asn | missense_variant | 18/22 | 1 | NM_005392.4 | P1 | |
PHF2 | ENST00000610682.1 | c.259G>A | p.Asp87Asn | missense_variant | 4/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152158Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD3 exomes AF: 0.000148 AC: 37AN: 250474Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135378
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GnomAD4 exome AF: 0.000264 AC: 385AN: 1459846Hom.: 1 Cov.: 31 AF XY: 0.000278 AC XY: 202AN XY: 725996
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GnomAD4 genome ? AF: 0.000250 AC: 38AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74442
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ExAC
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.2563G>A (p.D855N) alteration is located in exon 18 (coding exon 18) of the PHF2 gene. This alteration results from a G to A substitution at nucleotide position 2563, causing the aspartic acid (D) at amino acid position 855 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.
REVEL
Benign
Sift
Uncertain
D;.;.
Sift4G
Benign
T;T;T
Polyphen
D;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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