X-134377626-C-T
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The ENST00000370803.8(PHF6):c.9C>T(p.Ser3=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000639 in 1,095,384 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000064 ( 0 hom. 4 hem. )
Consequence
PHF6
ENST00000370803.8 synonymous
ENST00000370803.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.75
Genes affected
PHF6 (HGNC:18145): (PHD finger protein 6) This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by cognitive disability, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant X-134377626-C-T is Benign according to our data. Variant chrX-134377626-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3031461.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Hemizygotes in GnomAdExome4 at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF6 | NM_001015877.2 | c.9C>T | p.Ser3= | synonymous_variant | 2/11 | ENST00000370803.8 | NP_001015877.1 | |
PHF6 | NM_032458.3 | c.9C>T | p.Ser3= | synonymous_variant | 2/10 | NP_115834.1 | ||
PHF6 | NM_032335.3 | c.9C>T | p.Ser3= | synonymous_variant | 2/8 | NP_115711.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHF6 | ENST00000370803.8 | c.9C>T | p.Ser3= | synonymous_variant | 2/11 | 1 | NM_001015877.2 | ENSP00000359839 | P4 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181747Hom.: 0 AF XY: 0.0000302 AC XY: 2AN XY: 66293
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GnomAD4 exome AF: 0.00000639 AC: 7AN: 1095384Hom.: 0 Cov.: 30 AF XY: 0.0000111 AC XY: 4AN XY: 361012
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GnomAD4 genome Cov.: 22
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
PHF6-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2021 | 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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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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