rs222851
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024297.3(PHF23):c.997+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 1,610,124 control chromosomes in the GnomAD database, including 137,148 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 16233 hom., cov: 33)
Exomes 𝑓: 0.40 ( 120915 hom. )
Consequence
PHF23
NM_024297.3 intron
NM_024297.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.169
Genes affected
PHF23 (HGNC:28428): (PHD finger protein 23) Predicted to enable metal ion binding activity. Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of protein ubiquitination. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF23 | NM_024297.3 | c.997+11C>T | intron_variant | ENST00000320316.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF23 | ENST00000320316.8 | c.997+11C>T | intron_variant | 1 | NM_024297.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.452 AC: 68635AN: 152000Hom.: 16225 Cov.: 33
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GnomAD3 exomes AF: 0.423 AC: 104528AN: 246890Hom.: 23417 AF XY: 0.411 AC XY: 55131AN XY: 134104
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GnomAD4 exome AF: 0.402 AC: 586098AN: 1458006Hom.: 120915 Cov.: 48 AF XY: 0.398 AC XY: 288528AN XY: 724506
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GnomAD4 genome ? AF: 0.451 AC: 68676AN: 152118Hom.: 16233 Cov.: 33 AF XY: 0.448 AC XY: 33317AN XY: 74358
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at