15-43403665-ACT-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001141980.3(TP53BP1):c.*3716_*3717delAG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000632 in 1,581,768 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001141980.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TP53BP1 | NM_001141980.3 | c.*3716_*3717delAG | 3_prime_UTR_variant | Exon 28 of 28 | ENST00000382044.9 | NP_001135452.1 | ||
TUBGCP4 | NM_014444.5 | c.1732-15_1732-14delCT | intron_variant | Intron 15 of 17 | ENST00000564079.6 | NP_055259.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TP53BP1 | ENST00000382044 | c.*3716_*3717delAG | 3_prime_UTR_variant | Exon 28 of 28 | 1 | NM_001141980.3 | ENSP00000371475.5 | |||
TUBGCP4 | ENST00000564079.6 | c.1732-15_1732-14delCT | intron_variant | Intron 15 of 17 | 1 | NM_014444.5 | ENSP00000456648.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151844Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247692Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134384
GnomAD4 exome AF: 0.00000560 AC: 8AN: 1429806Hom.: 0 AF XY: 0.00000701 AC XY: 5AN XY: 713002
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change falls in intron 15 of the TUBGCP4 gene. It does not directly change the encoded amino acid sequence of the TUBGCP4 protein. This variant is present in population databases (rs757987955, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with TUBGCP4-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at