NM_001372066.1:c.452T>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS2
The NM_001372066.1(TFAP2A):c.452T>A(p.Ile151Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000356 in 1,404,108 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001372066.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFAP2A | NM_001372066.1 | c.452T>A | p.Ile151Asn | missense_variant | Exon 2 of 7 | ENST00000379613.10 | NP_001358995.1 | |
TFAP2A | NM_001042425.3 | c.434T>A | p.Ile145Asn | missense_variant | Exon 2 of 7 | NP_001035890.1 | ||
TFAP2A | NM_001032280.3 | c.428T>A | p.Ile143Asn | missense_variant | Exon 2 of 7 | NP_001027451.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFAP2A | ENST00000379613.10 | c.452T>A | p.Ile151Asn | missense_variant | Exon 2 of 7 | 1 | NM_001372066.1 | ENSP00000368933.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 2AN: 162622Hom.: 0 AF XY: 0.0000116 AC XY: 1AN XY: 86370
GnomAD4 exome AF: 0.00000356 AC: 5AN: 1404108Hom.: 0 Cov.: 32 AF XY: 0.00000144 AC XY: 1AN XY: 693084
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TFAP2A protein function. ClinVar contains an entry for this variant (Variation ID: 1956629). This variant has not been reported in the literature in individuals affected with TFAP2A-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.008%). This sequence change replaces isoleucine, which is neutral and non-polar, with asparagine, which is neutral and polar, at codon 149 of the TFAP2A protein (p.Ile149Asn). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at