chr20-46687082-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_033550.4(TP53RK):āc.433A>Gā(p.Thr145Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,614,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_033550.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TP53RK | NM_033550.4 | c.433A>G | p.Thr145Ala | missense_variant | 2/2 | ENST00000372114.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TP53RK | ENST00000372114.4 | c.433A>G | p.Thr145Ala | missense_variant | 2/2 | 1 | NM_033550.4 | P1 | |
TP53RK | ENST00000372102.3 | c.*72A>G | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000812 AC: 204AN: 251372Hom.: 1 AF XY: 0.000684 AC XY: 93AN XY: 135904
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 727248
GnomAD4 genome AF: 0.000407 AC: 62AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000497 AC XY: 37AN XY: 74458
ClinVar
Submissions by phenotype
Galloway-Mowat syndrome 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 20, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
TP53RK-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2019 | This variant is classified as 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