X-136876650-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002139.4(RBMX):c.394G>T(p.Gly132Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,171,468 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002139.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBMX | NM_002139.4 | c.394G>T | p.Gly132Cys | missense_variant | Exon 5 of 9 | ENST00000320676.11 | NP_002130.2 | |
RBMX | NM_001164803.2 | c.217-1065G>T | intron_variant | Intron 3 of 7 | NP_001158275.1 | |||
RBMX | NR_028476.2 | n.377G>T | non_coding_transcript_exon_variant | Exon 4 of 8 | ||||
RBMX | NR_028477.2 | n.584G>T | non_coding_transcript_exon_variant | Exon 5 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000546 AC: 6AN: 109922Hom.: 0 Cov.: 21 AF XY: 0.0000620 AC XY: 2AN XY: 32238
GnomAD3 exomes AF: 0.0000449 AC: 7AN: 155766Hom.: 0 AF XY: 0.0000190 AC XY: 1AN XY: 52714
GnomAD4 exome AF: 0.000114 AC: 121AN: 1061500Hom.: 0 Cov.: 29 AF XY: 0.0000736 AC XY: 25AN XY: 339654
GnomAD4 genome AF: 0.0000546 AC: 6AN: 109968Hom.: 0 Cov.: 21 AF XY: 0.0000619 AC XY: 2AN XY: 32294
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.394G>T (p.G132C) alteration is located in exon 5 (coding exon 4) of the RBMX gene. This alteration results from a G to T substitution at nucleotide position 394, causing the glycine (G) at amino acid position 132 to be replaced by a cysteine (C). 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