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GeneBe

1-151760884-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_031420.4(MRPL9):​c.604G>A​(p.Ala202Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000757 in 1,320,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 24)
Exomes 𝑓: 7.6e-7 ( 0 hom. )

Consequence

MRPL9
NM_031420.4 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.82
Variant links:
Genes affected
MRPL9 (HGNC:14277): (mitochondrial ribosomal protein L9) This is a nuclear gene encoding a protein component of the 39S subunit of the mitochondrial ribosome. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Jul 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.10670629).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL9NM_031420.4 linkuse as main transcriptc.604G>A p.Ala202Thr missense_variant 6/7 ENST00000368830.8
MRPL9NM_001300733.2 linkuse as main transcriptc.502G>A p.Ala168Thr missense_variant 5/6
MRPL9NR_125331.2 linkuse as main transcriptn.661G>A non_coding_transcript_exon_variant 6/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL9ENST00000368830.8 linkuse as main transcriptc.604G>A p.Ala202Thr missense_variant 6/71 NM_031420.4 P1

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
AF:
7.57e-7
AC:
1
AN:
1320620
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
660866
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:
0.00
Gnomad4 NFE exome
AF:
9.88e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
24

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 12, 2021The c.604G>A (p.A202T) alteration is located in exon 6 (coding exon 6) of the MRPL9 gene. This alteration results from a G to A substitution at nucleotide position 604, causing the alanine (A) at amino acid position 202 to be replaced by a threonine (T). 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
0.13
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
18
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0029
T;.
Eigen
Benign
-0.39
Eigen_PC
Benign
-0.27
FATHMM_MKL
Benign
0.74
D
LIST_S2
Benign
0.82
T;T
M_CAP
Benign
0.0050
T
MetaRNN
Benign
0.11
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.7
L;.
MutationTaster
Benign
0.82
D;D
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-0.47
N;N
REVEL
Benign
0.018
Sift
Uncertain
0.020
D;D
Sift4G
Benign
0.18
T;T
Polyphen
0.048
B;.
Vest4
0.054
MutPred
0.28
Gain of methylation at K207 (P = 0.1147);.;
MVP
0.34
MPC
0.53
ClinPred
0.38
T
GERP RS
3.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.045
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-151733360; API