rs199945885
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001015877.2(PHF6):c.487C>T(p.Arg163Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000472 in 1,208,663 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001015877.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PHF6 | NM_001015877.2 | c.487C>T | p.Arg163Cys | missense_variant | Exon 6 of 11 | ENST00000370803.8 | NP_001015877.1 | |
PHF6 | NM_032458.3 | c.487C>T | p.Arg163Cys | missense_variant | Exon 6 of 10 | NP_115834.1 | ||
PHF6 | NM_032335.3 | c.490C>T | p.Arg164Cys | missense_variant | Exon 6 of 8 | NP_115711.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000720 AC: 8AN: 111183Hom.: 0 Cov.: 23 AF XY: 0.0000897 AC XY: 3AN XY: 33453
GnomAD3 exomes AF: 0.0000603 AC: 11AN: 182563Hom.: 0 AF XY: 0.0000595 AC XY: 4AN XY: 67221
GnomAD4 exome AF: 0.0000446 AC: 49AN: 1097426Hom.: 0 Cov.: 31 AF XY: 0.0000441 AC XY: 16AN XY: 362878
GnomAD4 genome AF: 0.0000719 AC: 8AN: 111237Hom.: 0 Cov.: 23 AF XY: 0.0000895 AC XY: 3AN XY: 33517
ClinVar
Submissions by phenotype
not provided Uncertain:2
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Borjeson-Forssman-Lehmann syndrome Benign:2
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PHF6-related disorder Uncertain:1
The PHF6 c.487C>T variant is predicted to result in the amino acid substitution p.Arg163Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including in 4 hemizygous individuals. Although we suspect this variant may possibly be benign, at this time its clinical significance is uncertain due to the absence of conclusive functional and genetic evidence. -
not specified Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at