2-160284996-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_016836.4(RBMS1):c.805G>A(p.Gly269Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016836.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBMS1 | NM_016836.4 | c.805G>A | p.Gly269Arg | missense_variant, splice_region_variant | Exon 8 of 14 | ENST00000348849.8 | NP_058520.1 | |
RBMS1 | NM_002897.5 | c.796G>A | p.Gly266Arg | missense_variant, splice_region_variant | Exon 8 of 14 | NP_002888.1 | ||
RBMS1 | XM_047445368.1 | c.805G>A | p.Gly269Arg | missense_variant, splice_region_variant | Exon 8 of 14 | XP_047301324.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251308Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135820
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460342Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726624
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.805G>A (p.G269R) alteration is located in exon 8 (coding exon 8) of the RBMS1 gene. This alteration results from a G to A substitution at nucleotide position 805, causing the glycine (G) at amino acid position 269 to be replaced by an arginine (R). 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