9-34179202-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001171201.1(UBAP1):c.188C>T(p.Thr63Ile) variant causes a missense 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_001171201.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -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 | 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 | 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
GnomAD4 exome AF: 0.0000277 AC: 30AN: 1082826Hom.: 0 Cov.: 33 AF XY: 0.0000235 AC XY: 12AN XY: 511626
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151392Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73862
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