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GeneBe

11-1956386-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_021134.4(MRPL23):c.428G>A(p.Arg143Gln) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 17)
Exomes 𝑓: 0.000013 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MRPL23
NM_021134.4 missense

Scores

2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.87

Links

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.1802808).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.428G>A p.Arg143Gln missense_variant 5/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.428G>A p.Arg143Gln missense_variant 5/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
1
AN:
131774
Hom.:
0
Cov.:
17
FAILED QC
Gnomad AFR
AF:
0.0000260
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
GnomAD3 exomes
AF:
0.0000126
AC:
3
AN:
237678
Hom.:
0
AF XY:
0.00000770
AC XY:
1
AN XY:
129858
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000277
Gnomad OTH exome
AF:
0.00
ExAC
AF:
0.00000827
AC:
1
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 16, 2023The c.428G>A (p.R143Q) alteration is located in exon 5 (coding exon 5) of the MRPL23 gene. This alteration results from a G to A substitution at nucleotide position 428, causing the arginine (R) at amino acid position 143 to be replaced by a glutamine (Q). 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
0.10
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.44
Cadd
Benign
16
Dann
Uncertain
0.98
DEOGEN2
Benign
0.0048
T;T
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.45
FATHMM_MKL
Uncertain
0.89
D
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.18
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
2.0
M;M
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Benign
0.39
T
PROVEAN
Benign
-1.2
N;N
REVEL
Benign
0.13
Sift
Benign
0.062
T;T
Sift4G
Benign
0.098
T;T
Polyphen
0.52
P;P
Vest4
0.24
MutPred
0.21
Loss of MoRF binding (P = 0.0286);Loss of MoRF binding (P = 0.0286);
MVP
0.41
MPC
0.20
ClinPred
0.23
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.14
gMVP
0.37

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: rs759082420; hg19: chr11-1977616; API