chr3-189631535-G-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_003722.5(TP63):c.20G>T(p.Arg7Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000124 in 1,612,730 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R7W) has been classified as Uncertain significance.
Frequency
Consequence
NM_003722.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TP63 | NM_003722.5 | c.20G>T | p.Arg7Leu | missense_variant | 1/14 | ENST00000264731.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TP63 | ENST00000264731.8 | c.20G>T | p.Arg7Leu | missense_variant | 1/14 | 1 | NM_003722.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000295 AC: 74AN: 251174Hom.: 3 AF XY: 0.000368 AC XY: 50AN XY: 135744
GnomAD4 exome AF: 0.000131 AC: 191AN: 1460570Hom.: 3 Cov.: 33 AF XY: 0.000171 AC XY: 124AN XY: 726646
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74372
ClinVar
Submissions by phenotype
TP63-Related Spectrum Disorders Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2022 | - - |
Ankyloblepharon-ectodermal defects-cleft lip/palate syndrome;C1785148:Rapp-Hodgkin ectodermal dysplasia syndrome;C1851878:Orofacial cleft 8;C1854442:Split hand-foot malformation 4;C1858562:Ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3;C1863204:ADULT syndrome;C1863753:Limb-mammary syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 02, 2021 | - - |
TP63-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 06, 2022 | 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