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GeneBe

11-1952827-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The NM_021134.4(MRPL23):c.269C>T(p.Pro90Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.000024 ( 0 hom. )

Consequence

MRPL23
NM_021134.4 missense

Scores

2
6
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.44

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.33801603).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.269C>T p.Pro90Leu missense_variant 4/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.269C>T p.Pro90Leu missense_variant 4/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD3 exomes
AF:
0.0000240
AC:
6
AN:
250084
Hom.:
0
AF XY:
0.0000295
AC XY:
4
AN XY:
135528
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.0000655
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000266
Gnomad OTH exome
AF:
0.00
Alfa
AF:
0.0000611
Hom.:
0
ExAC
AF:
0.0000247
AC:
3

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 GeneticsMay 26, 2023The c.269C>T (p.P90L) alteration is located in exon 4 (coding exon 4) of the MRPL23 gene. This alteration results from a C to T substitution at nucleotide position 269, causing the proline (P) at amino acid position 90 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
0.25
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.21
Cadd
Benign
21
Dann
Uncertain
1.0
DEOGEN2
Benign
0.081
T;T;T;T;T
Eigen
Benign
0.18
Eigen_PC
Benign
0.099
FATHMM_MKL
Uncertain
0.93
D
M_CAP
Uncertain
0.10
D
MetaRNN
Benign
0.34
T;T;T;T;T
MetaSVM
Benign
-0.56
T
MutationAssessor
Pathogenic
3.1
M;M;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Uncertain
0.72
T
PROVEAN
Pathogenic
-5.8
D;D;D;D;D
REVEL
Benign
0.25
Sift
Uncertain
0.028
D;D;D;D;D
Sift4G
Uncertain
0.021
D;D;D;D;D
Polyphen
0.80
P;P;.;.;.
Vest4
0.42
MutPred
0.48
Loss of disorder (P = 0.0419);Loss of disorder (P = 0.0419);Loss of disorder (P = 0.0419);Loss of disorder (P = 0.0419);Loss of disorder (P = 0.0419);
MVP
0.67
MPC
0.36
ClinPred
0.93
D
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.74
gMVP
0.47

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: rs776496538; hg19: chr11-1974057; API