6-10398435-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001372066.1(TFAP2A):c.1302G>A(p.Glu434Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,614,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001372066.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFAP2A | NM_001372066.1 | c.1302G>A | p.Glu434Glu | synonymous_variant | Exon 7 of 7 | ENST00000379613.10 | NP_001358995.1 | |
TFAP2A | NM_001042425.3 | c.1284G>A | p.Glu428Glu | synonymous_variant | Exon 7 of 7 | NP_001035890.1 | ||
TFAP2A | NM_001032280.3 | c.1278G>A | p.Glu426Glu | synonymous_variant | Exon 7 of 7 | NP_001027451.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFAP2A | ENST00000379613.10 | c.1302G>A | p.Glu434Glu | synonymous_variant | Exon 7 of 7 | 1 | NM_001372066.1 | ENSP00000368933.5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249758Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135080
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461878Hom.: 0 Cov.: 38 AF XY: 0.000120 AC XY: 87AN XY: 727240
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
TFAP2A-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at