NM_001030.6:c.6+15C>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_001030.6(RPS27):c.6+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,614,076 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 (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
RPS27
NM_001030.6 intron
NM_001030.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0810
Genes affected
RPS27 (HGNC:10416): (ribosomal protein S27) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the S27e family of ribosomal proteins and component of the 40S subunit. The encoded protein contains a C4-type zinc finger domain that can bind to zinc and may bind to nucleic acid. Mutations in this gene have been identified in numerous melanoma patients and in at least one patient with Diamond-Blackfan anemia (DBA). Elevated expression of this gene has been observed in various human cancers. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2018]
RAB13 (HGNC:9762): (RAB13, member RAS oncogene family) This gene is a member of the Rab family of small G proteins and plays a role in regulating membrane trafficking between trans-Golgi network (TGN) and recycling endosomes (RE). The encoded protein is involved in the assembly of tight junctions, which are components of the apical junctional complex (AJC) of epithelial cells. The AJC plays a role in forming a barrier between luminal contents and the underlying tissue. Additional functions associated with the protein include endocytic recycling of occludin, regulation of epithelial cell scattering, neuronal regeneration and regulation of neurite outgrowth. Alternately spliced transcript variants have been observed for this gene. A pseudogene associated with this gene is located on chromosome 12. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.15).
BP6
Variant 1-153990817-C-T is Benign according to our data. Variant chr1-153990817-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1973866.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS27 | NM_001030.6 | c.6+15C>T | intron_variant | Intron 1 of 3 | ENST00000651669.1 | NP_001021.1 | ||
RPS27 | NM_001349947.2 | c.-308C>T | 5_prime_UTR_variant | Exon 1 of 4 | NP_001336876.1 | |||
RPS27 | NM_001349946.2 | c.-212+15C>T | intron_variant | Intron 1 of 4 | NP_001336875.1 | |||
RAB13 | XM_017001959.2 | c.-310G>A | upstream_gene_variant | XP_016857448.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152210Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000111 AC: 28AN: 251488Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135920
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GnomAD4 exome AF: 0.000124 AC: 181AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 727236
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GnomAD4 genome AF: 0.0000788 AC: 12AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74350
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 08, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at