3-51391656-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_013286.5(RBM15B):​c.257C>T​(p.Ser86Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,201,430 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000080 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000067 ( 0 hom. )

Consequence

RBM15B
NM_013286.5 missense

Scores

1
2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0480
Variant links:
Genes affected
RBM15B (HGNC:24303): (RNA binding motif protein 15B) Members of the SPEN (Split-end) family of proteins, including RBM15B, have repressor function in several signaling pathways and may bind to RNA through interaction with spliceosome components (Hiriart et al., 2005 [PubMed 16129689]).[supplied by OMIM, Feb 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.06878826).
BS2
High AC in GnomAd4 at 12 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RBM15BNM_013286.5 linkc.257C>T p.Ser86Leu missense_variant Exon 1 of 1 ENST00000563281.2 NP_037418.3 Q8NDT2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RBM15BENST00000563281.2 linkc.257C>T p.Ser86Leu missense_variant Exon 1 of 1 6 NM_013286.5 ENSP00000454545.1 Q8NDT2-1

Frequencies

GnomAD3 genomes
AF:
0.0000798
AC:
12
AN:
150424
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000291
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000666
AC:
7
AN:
1051006
Hom.:
0
Cov.:
31
AF XY:
0.0000101
AC XY:
5
AN XY:
496128
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000137
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000513
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000443
Gnomad4 OTH exome
AF:
0.0000242
GnomAD4 genome
AF:
0.0000798
AC:
12
AN:
150424
Hom.:
0
Cov.:
32
AF XY:
0.0000545
AC XY:
4
AN XY:
73360
show subpopulations
Gnomad4 AFR
AF:
0.000291
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.0000982

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 26, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.257C>T (p.S86L) alteration is located in exon 1 (coding exon 1) of the RBM15B gene. This alteration results from a C to T substitution at nucleotide position 257, causing the serine (S) at amino acid position 86 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.039
T
Eigen
Benign
-1.0
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.030
N
LIST_S2
Benign
0.60
T
M_CAP
Benign
0.061
D
MetaRNN
Benign
0.069
T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.34
N
PrimateAI
Pathogenic
0.93
D
PROVEAN
Benign
-0.95
N
Sift
Uncertain
0.0040
D
Sift4G
Benign
0.24
T
Polyphen
0.0030
B
Vest4
0.091
MutPred
0.29
Loss of phosphorylation at S86 (P = 9e-04);
MVP
0.18
ClinPred
0.092
T
GERP RS
0.53
Varity_R
0.081
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1273441919; hg19: chr3-51429087; API