16-2254004-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_080594.4(RNPS1):c.878G>A(p.Arg293His) variant causes a missense change. The variant allele was found at a frequency of 0.0000391 in 1,534,198 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_080594.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNPS1 | ENST00000320225.10 | c.878G>A | p.Arg293His | missense_variant | Exon 8 of 8 | 1 | NM_080594.4 | ENSP00000315859.5 | ||
RNPS1 | ENST00000301730.12 | c.878G>A | p.Arg293His | missense_variant | Exon 9 of 9 | 2 | ENSP00000301730.8 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000506 AC: 7AN: 138336Hom.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 72862
GnomAD4 exome AF: 0.0000398 AC: 55AN: 1382014Hom.: 0 Cov.: 30 AF XY: 0.0000382 AC XY: 26AN XY: 680390
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.878G>A (p.R293H) alteration is located in exon 8 (coding exon 7) of the RNPS1 gene. This alteration results from a G to A substitution at nucleotide position 878, causing the arginine (R) at amino acid position 293 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