rs793888540
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PM5PP3_StrongPP5_Moderate
The NM_001372066.1(TFAP2A):c.655C>A(p.Arg219Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R219L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001372066.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFAP2A | NM_001372066.1 | c.655C>A | p.Arg219Ser | missense_variant | 4/7 | ENST00000379613.10 | |
TFAP2A-AS2 | NR_145448.1 | n.122G>T | non_coding_transcript_exon_variant | 1/1 | |||
TFAP2A | NM_001042425.3 | c.637C>A | p.Arg213Ser | missense_variant | 4/7 | ||
TFAP2A | NM_001032280.3 | c.631C>A | p.Arg211Ser | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFAP2A | ENST00000379613.10 | c.655C>A | p.Arg219Ser | missense_variant | 4/7 | 1 | NM_001372066.1 | A1 | |
TFAP2A-AS2 | ENST00000645232.1 | n.122G>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Branchiooculofacial syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at