chr20-35917521-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_016436.5(PHF20):c.1863T>C(p.Phe621=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000929 in 1,614,082 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 12 hom. )
Consequence
PHF20
NM_016436.5 synonymous
NM_016436.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.241
Genes affected
PHF20 (HGNC:16098): (PHD finger protein 20) Predicted to enable DNA binding activity and metal ion binding activity. Involved in histone H4-K16 acetylation; histone H4-K5 acetylation; and histone H4-K8 acetylation. Located in cytosol; nuclear membrane; and nucleoplasm. Part of MLL1 complex and histone acetyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 20-35917521-T-C is Benign according to our data. Variant chr20-35917521-T-C is described in ClinVar as [Benign]. Clinvar id is 717046.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.241 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00471 (717/152306) while in subpopulation AFR AF= 0.0165 (685/41564). AF 95% confidence interval is 0.0155. There are 6 homozygotes in gnomad4. There are 346 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 711 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF20 | NM_016436.5 | c.1863T>C | p.Phe621= | synonymous_variant | 13/18 | ENST00000374012.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF20 | ENST00000374012.8 | c.1863T>C | p.Phe621= | synonymous_variant | 13/18 | 1 | NM_016436.5 | P1 | |
PHF20 | ENST00000420233.1 | c.54T>C | p.Phe18= | synonymous_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00467 AC: 711AN: 152188Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00115 AC: 288AN: 251232Hom.: 1 AF XY: 0.000876 AC XY: 119AN XY: 135802
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GnomAD4 exome AF: 0.000536 AC: 783AN: 1461776Hom.: 12 Cov.: 31 AF XY: 0.000484 AC XY: 352AN XY: 727180
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 18, 2018 | - - |
Computational scores
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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