1-228165807-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010867.4(IBA57):c.-10C>G 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 0.0000348 in 1,294,280 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_001010867.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IBA57 | NM_001010867.4 | c.-10C>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 3 | ENST00000366711.4 | NP_001010867.1 | ||
IBA57 | NM_001010867.4 | c.-10C>G | 5_prime_UTR_variant | Exon 1 of 3 | ENST00000366711.4 | NP_001010867.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IBA57 | ENST00000366711 | c.-10C>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 3 | 2 | NM_001010867.4 | ENSP00000355672.3 | |||
IBA57 | ENST00000366711 | c.-10C>G | 5_prime_UTR_variant | Exon 1 of 3 | 2 | NM_001010867.4 | ENSP00000355672.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000350 AC: 40AN: 1142132Hom.: 0 Cov.: 30 AF XY: 0.0000237 AC XY: 13AN XY: 547828
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: C1orf69 (IBA57) c.-10C>G is located in the untranscribed region upstream of the C1orf69 gene region. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes a 3' acceptor site. Two predict the variant weakens a 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2e-05 in 48802 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.-10C>G in individuals affected with C1orf69-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. 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