chr6-132817027-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001016.4(RPS12):c.302G>A(p.Arg101His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,611,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001016.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS12 | ENST00000230050.4 | c.302G>A | p.Arg101His | missense_variant | Exon 5 of 6 | 1 | NM_001016.4 | ENSP00000230050.3 | ||
RPS12 | ENST00000484616.2 | n.520G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 2 | |||||
SNORA33 | ENST00000363664.1 | n.-192G>A | upstream_gene_variant | 6 | ||||||
SNORD100 | ENST00000408573.1 | n.*150G>A | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152056Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251358Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135848
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1459866Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726358
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152056Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302G>A (p.R101H) alteration is located in exon 5 (coding exon 4) of the RPS12 gene. This alteration results from a G to A substitution at nucleotide position 302, causing the arginine (R) at amino acid position 101 to be replaced by a histidine (H). 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