9-34179202-C-T
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_016525.5(UBAP1):c.-46C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,234,218 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 Uncertain significance (★).
Frequency
Consequence
NM_016525.5 5_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- spastic paraplegia 80, autosomal dominantInheritance: AD Classification: STRONG Submitted by: Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- hereditary spastic paraplegia 12Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Tourette syndromeInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBAP1 | NM_016525.5 | c.-46C>T | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000297661.9 | NP_057609.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBAP1 | ENST00000297661.9 | c.-46C>T | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_016525.5 | ENSP00000297661.4 | |||
UBAP1 | ENST00000625521.2 | c.188C>T | p.Thr63Ile | missense_variant | Exon 1 of 6 | 2 | ENSP00000486574.1 | |||
UBAP1 | ENST00000626262.2 | c.158C>T | p.Thr53Ile | missense_variant | Exon 1 of 6 | 2 | ENSP00000487222.1 | |||
UBAP1 | ENST00000379186.8 | c.-46C>T | 5_prime_UTR_variant | Exon 1 of 6 | 5 | ENSP00000368484.3 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151392Hom.: 0 Cov.: 31 show subpopulations
GnomAD4 exome AF: 0.0000277 AC: 30AN: 1082826Hom.: 0 Cov.: 33 AF XY: 0.0000235 AC XY: 12AN XY: 511626 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151392Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73862 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.188C>T (p.T63I) alteration is located in exon 1 (coding exon 1) of the UBAP1 gene. This alteration results from a C to T substitution at nucleotide position 188, causing the threonine (T) at amino acid position 63 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at