X-48898494-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001032382.2(PQBP1):c.-16C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000898 in 111,389 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001032382.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PQBP1 | NM_001032382.2 | c.-16C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 7 | ENST00000447146.7 | NP_001027554.1 | ||
PQBP1 | NM_001032382.2 | c.-16C>T | splice_region_variant | Exon 2 of 7 | ENST00000447146.7 | NP_001027554.1 | ||
PQBP1 | NM_001032382.2 | c.-16C>T | 5_prime_UTR_variant | Exon 2 of 7 | ENST00000447146.7 | NP_001027554.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PQBP1 | ENST00000447146 | c.-16C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 7 | 1 | NM_001032382.2 | ENSP00000391759.2 | |||
PQBP1 | ENST00000447146.7 | c.-16C>T | splice_region_variant | Exon 2 of 7 | 1 | NM_001032382.2 | ENSP00000391759.2 | |||
PQBP1 | ENST00000447146 | c.-16C>T | 5_prime_UTR_variant | Exon 2 of 7 | 1 | NM_001032382.2 | ENSP00000391759.2 |
Frequencies
GnomAD3 genomes AF: 0.00000898 AC: 1AN: 111389Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33569
GnomAD4 exome Cov.: 29
GnomAD4 genome AF: 0.00000898 AC: 1AN: 111389Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33569
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: PQBP1 c.-16C>T is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 8.3e-07 in 1207520 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-16C>T in individuals affected with Renpenning syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at