chr1-153990790-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001030.6(RPS27):c.-7C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,614,100 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 Likely benign (no stars).
Frequency
Consequence
NM_001030.6 5_prime_UTR
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 |
---|---|---|---|---|---|---|---|---|
RPS27 | NM_001030.6 | c.-7C>G | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000651669.1 | NP_001021.1 | ||
RPS27 | NM_001349946.2 | c.-224C>G | 5_prime_UTR_variant | Exon 1 of 5 | NP_001336875.1 | |||
RPS27 | NM_001349947.2 | c.-335C>G | 5_prime_UTR_variant | Exon 1 of 4 | NP_001336876.1 | |||
RAB13 | XM_017001959.2 | c.-283G>C | upstream_gene_variant | XP_016857448.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251486Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135918
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727248
GnomAD4 genome AF: 0.000197 AC: 30AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74358
ClinVar
Submissions by phenotype
RPS27-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at