chr5-146233680-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018989.2(RBM27):c.1081A>T(p.Met361Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000222 in 1,523,954 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M361V) has been classified as Uncertain significance.
Frequency
Consequence
NM_018989.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM27 | NM_018989.2 | c.1081A>T | p.Met361Leu | missense_variant | 7/21 | ENST00000265271.7 | |
LOC127814297 | NM_001414499.1 | c.1081A>T | p.Met361Leu | missense_variant | 7/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM27 | ENST00000265271.7 | c.1081A>T | p.Met361Leu | missense_variant | 7/21 | 1 | NM_018989.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00121 AC: 184AN: 151510Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000266 AC: 51AN: 191906Hom.: 0 AF XY: 0.000225 AC XY: 24AN XY: 106444
GnomAD4 exome AF: 0.000112 AC: 154AN: 1372324Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 82AN XY: 678952
GnomAD4 genome ? AF: 0.00121 AC: 184AN: 151630Hom.: 2 Cov.: 32 AF XY: 0.00116 AC XY: 86AN XY: 74144
ClinVar
Submissions by phenotype
RBM27-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at