chr13-49520866-T-TACAATTCTTTGAAATTAAATATTTC
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001040443.3(PHF11):c.459-26_459-2dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,458,018 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.00068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000051 ( 0 hom. )
Consequence
PHF11
NM_001040443.3 intron
NM_001040443.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.820
Genes affected
PHF11 (HGNC:17024): (PHD finger protein 11) This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 13-49520866-T-TACAATTCTTTGAAATTAAATATTTC is Benign according to our data. Variant chr13-49520866-T-TACAATTCTTTGAAATTAAATATTTC is described in ClinVar as [Likely_benign]. Clinvar id is 3052776.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF11 | NM_001040443.3 | c.459-26_459-2dup | intron_variant | ENST00000378319.8 | |||
SETDB2-PHF11 | NR_135324.2 | n.2905-26_2905-2dup | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF11 | ENST00000378319.8 | c.459-26_459-2dup | intron_variant | 1 | NM_001040443.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000683 AC: 104AN: 152218Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000128 AC: 28AN: 218322Hom.: 0 AF XY: 0.000109 AC XY: 13AN XY: 119366
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GnomAD4 exome AF: 0.0000505 AC: 66AN: 1305682Hom.: 0 Cov.: 18 AF XY: 0.0000321 AC XY: 21AN XY: 654540
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GnomAD4 genome AF: 0.000683 AC: 104AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74492
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PHF11-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BranchPoint Hunter
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at