rs79167802
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000281722.8(RBM46):āc.378T>Gā(p.Ile126Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 1,613,818 control chromosomes in the GnomAD database, including 751 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.018 ( 76 hom., cov: 32)
Exomes š: 0.020 ( 675 hom. )
Consequence
RBM46
ENST00000281722.8 missense
ENST00000281722.8 missense
Scores
1
10
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.62
Genes affected
RBM46 (HGNC:28401): (RNA binding motif protein 46) Predicted to enable mRNA binding activity. Predicted to act upstream of or within mRNA stabilization and trophectodermal cell differentiation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.00208053).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM46 | NM_144979.5 | c.378T>G | p.Ile126Met | missense_variant | 3/5 | ENST00000281722.8 | NP_659416.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM46 | ENST00000281722.8 | c.378T>G | p.Ile126Met | missense_variant | 3/5 | 1 | NM_144979.5 | ENSP00000281722 | A1 | |
RBM46 | ENST00000514866.5 | c.378T>G | p.Ile126Met | missense_variant | 3/6 | 2 | ENSP00000424500 | P4 | ||
RBM46 | ENST00000510397.5 | c.378T>G | p.Ile126Met | missense_variant | 3/5 | 2 | ENSP00000422813 | |||
RBM46 | ENST00000512640.1 | c.378T>G | p.Ile126Met | missense_variant | 3/3 | 4 | ENSP00000426672 |
Frequencies
GnomAD3 genomes AF: 0.0182 AC: 2769AN: 152172Hom.: 76 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0268 AC: 6734AN: 251004Hom.: 212 AF XY: 0.0268 AC XY: 3632AN XY: 135700
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GnomAD4 exome AF: 0.0199 AC: 29040AN: 1461528Hom.: 675 Cov.: 32 AF XY: 0.0200 AC XY: 14519AN XY: 727030
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GnomAD4 genome AF: 0.0182 AC: 2771AN: 152290Hom.: 76 Cov.: 32 AF XY: 0.0197 AC XY: 1468AN XY: 74468
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;.
MutationTaster
Benign
P;P;P
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;T
Polyphen
0.99
.;D;.;.
Vest4
MPC
2.3
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at