chr12-130434879-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001393629.1(RIMBP2):āc.2108T>Cā(p.Leu703Ser) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000281 in 1,603,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001393629.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIMBP2 | NM_001393629.1 | c.2108T>C | p.Leu703Ser | missense_variant, splice_region_variant | 14/23 | ENST00000690449.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIMBP2 | ENST00000690449.1 | c.2108T>C | p.Leu703Ser | missense_variant, splice_region_variant | 14/23 | NM_001393629.1 | P5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 32AN: 242626Hom.: 0 AF XY: 0.000114 AC XY: 15AN XY: 131436
GnomAD4 exome AF: 0.0000276 AC: 40AN: 1451052Hom.: 0 Cov.: 31 AF XY: 0.0000222 AC XY: 16AN XY: 721070
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.2057T>C (p.L686S) alteration is located in exon 11 (coding exon 9) of the RIMBP2 gene. This alteration results from a T to C substitution at nucleotide position 2057, causing the leucine (L) at amino acid position 686 to be replaced by a serine (S). 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