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GeneBe

11-1950912-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_021134.4(MRPL23):c.31C>T(p.Arg11Trp) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R11Q) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0 ( 1 hom., cov: 5)
Exomes 𝑓: 0.00014 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MRPL23
NM_021134.4 missense

Scores

1
7
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.27

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.019785672).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.31C>T p.Arg11Trp missense_variant 2/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.31C>T p.Arg11Trp missense_variant 2/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
6
AN:
31280
Hom.:
1
Cov.:
5
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.0116
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:
0.000136
AC:
34
AN:
250874
Hom.:
0
AF XY:
0.000125
AC XY:
17
AN XY:
135724
show subpopulations
Gnomad AFR exome
AF:
0.0000616
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00238
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000707
Gnomad OTH exome
AF:
0.00
Alfa
AF:
0.000230
Hom.:
0
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000906
AC:
11
EpiCase
AF:
0.000218
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 GeneticsMar 31, 2023The c.31C>T (p.R11W) alteration is located in exon 2 (coding exon 2) of the MRPL23 gene. This alteration results from a C to T substitution at nucleotide position 31, causing the arginine (R) at amino acid position 11 to be replaced by a tryptophan (W). 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
0.20
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.37
Cadd
Uncertain
25
Dann
Pathogenic
1.0
DEOGEN2
Benign
0.032
T;T;T;T;T
Eigen
Uncertain
0.19
Eigen_PC
Uncertain
0.24
FATHMM_MKL
Uncertain
0.89
D
M_CAP
Benign
0.042
D
MetaRNN
Benign
0.020
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;.;.;.
MutationTaster
Benign
0.79
D;D;D;D;D
PrimateAI
Uncertain
0.78
T
PROVEAN
Uncertain
-2.7
D;D;D;D;D
REVEL
Benign
0.20
Sift
Uncertain
0.0010
D;D;D;D;D
Sift4G
Uncertain
0.017
D;D;D;D;D
Polyphen
0.99
D;D;.;.;.
Vest4
0.29
MVP
0.39
MPC
0.36
ClinPred
0.35
T
GERP RS
4.5
Varity_R
0.72
gMVP
0.50

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: rs375605257; hg19: chr11-1972142; API