chr11-45934081-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_001352027.3(PHF21A):c.1933T>C(p.Ser645Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,461,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001352027.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHF21A | NM_001352027.3 | c.1933T>C | p.Ser645Pro | missense_variant | 19/19 | ENST00000676320.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHF21A | ENST00000676320.1 | c.1933T>C | p.Ser645Pro | missense_variant | 19/19 | NM_001352027.3 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461622Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727130
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 26, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at