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GeneBe

11-1950990-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.109G>A(p.Glu37Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 6)
Exomes 𝑓: 0.00011 ( 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: 3.22

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=0.1342541).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL23NM_021134.4 linkuse as main transcriptc.109G>A p.Glu37Lys missense_variant 2/5 ENST00000397298.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL23ENST00000397298.8 linkuse as main transcriptc.109G>A p.Glu37Lys missense_variant 2/51 NM_021134.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
8
AN:
46966
Hom.:
0
Cov.:
6
FAILED QC
Gnomad AFR
AF:
0.00
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:
0.000563
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000256
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000107
AC:
25
AN:
233684
Hom.:
0
AF XY:
0.000103
AC XY:
13
AN XY:
126564
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:
0.000549
Gnomad NFE exome
AF:
0.000125
Gnomad OTH exome
AF:
0.000172
GnomAD4 exome
AF:
0.0000859
AC:
17
AN:
197978
Hom.:
1
AF XY:
0.0000978
AC XY:
10
AN XY:
102270
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000465
Gnomad4 NFE exome
AF:
0.0000558
Gnomad4 OTH exome
AF:
0.000257
Alfa
AF:
0.000352
Hom.:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000107
AC:
13

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 GeneticsAug 02, 2022The c.109G>A (p.E37K) alteration is located in exon 2 (coding exon 2) of the MRPL23 gene. This alteration results from a G to A substitution at nucleotide position 109, causing the glutamic acid (E) at amino acid position 37 to be replaced by a lysine (K). 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
0.11
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.41
Cadd
Benign
22
Dann
Uncertain
1.0
DEOGEN2
Benign
0.0022
T;T;T;T;T
Eigen
Benign
0.12
Eigen_PC
Benign
0.15
FATHMM_MKL
Benign
0.72
D
M_CAP
Benign
0.0096
T
MetaRNN
Benign
0.13
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.1
L;L;.;.;.
MutationTaster
Benign
0.91
N;N;N;N;N
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
-0.61
N;N;N;N;N
REVEL
Benign
0.075
Sift
Benign
0.36
T;T;T;T;T
Sift4G
Benign
0.14
T;T;T;T;T
Polyphen
0.94
P;P;.;.;.
Vest4
0.53
MVP
0.48
MPC
0.25
ClinPred
0.11
T
GERP RS
4.5
Varity_R
0.36
gMVP
0.36

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: rs199601271; hg19: chr11-1972220; COSMIC: COSV67413689; COSMIC: COSV67413689; API