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GeneBe

11-1950951-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3

The NM_021134.4(MRPL23):c.70T>G(p.Phe24Val) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 5)

Consequence

MRPL23
NM_021134.4 missense

Scores

3
10
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.41

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.759

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.70T>G p.Phe24Val missense_variant 2/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.70T>G p.Phe24Val missense_variant 2/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
Cov.:
5

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 GeneticsNov 23, 2021The c.70T>G (p.F24V) alteration is located in exon 2 (coding exon 2) of the MRPL23 gene. This alteration results from a T to G substitution at nucleotide position 70, causing the phenylalanine (F) at amino acid position 24 to be replaced by a valine (V). 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
Pathogenic
0.64
BayesDel_addAF
Uncertain
0.027
T
BayesDel_noAF
Benign
-0.20
Cadd
Pathogenic
26
Dann
Uncertain
0.99
DEOGEN2
Benign
0.064
T;T;T;T;T
Eigen
Uncertain
0.64
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Uncertain
0.90
D
M_CAP
Benign
0.038
D
MetaRNN
Pathogenic
0.76
D;D;D;D;D
MetaSVM
Benign
-0.79
T
MutationAssessor
Uncertain
2.8
M;M;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Uncertain
0.72
T
PROVEAN
Pathogenic
-6.3
D;D;D;D;D
REVEL
Uncertain
0.31
Sift
Uncertain
0.0020
D;D;D;D;D
Sift4G
Uncertain
0.0020
D;D;D;D;D
Polyphen
0.99
D;D;.;.;.
Vest4
0.76
MutPred
0.70
Loss of stability (P = 0.0706);Loss of stability (P = 0.0706);Loss of stability (P = 0.0706);Loss of stability (P = 0.0706);Loss of stability (P = 0.0706);
MVP
0.52
MPC
0.63
ClinPred
0.99
D
GERP RS
4.5
Varity_R
0.97
gMVP
0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-1972181; API