X-130402255-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_016024.4(RBMX2):c.6C>T(p.Asn2Asn) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,023,508 control chromosomes in the GnomAD database, including 1 homozygotes. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_016024.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBMX2 | ENST00000305536.11 | c.6C>T | p.Asn2Asn | splice_region_variant, synonymous_variant | Exon 2 of 6 | 1 | NM_016024.4 | ENSP00000339090.4 | ||
RBMX2 | ENST00000469953.1 | n.255C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | |||||
RBMX2 | ENST00000370947.1 | c.6C>T | p.Asn2Asn | splice_region_variant, synonymous_variant | Exon 2 of 3 | 2 | ENSP00000359985.1 |
Frequencies
GnomAD3 genomes Cov.: 18
GnomAD3 exomes AF: 0.00000592 AC: 1AN: 168873Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 56679
GnomAD4 exome AF: 0.0000107 AC: 11AN: 1023508Hom.: 1 Cov.: 43 AF XY: 0.00000618 AC XY: 2AN XY: 323696
GnomAD4 genome Cov.: 18
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at