chr11-1952119-G-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_021134.4(MRPL23):c.141-8G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00046 ( 0 hom., cov: 2)
Exomes 𝑓: 0.00028 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MRPL23
NM_021134.4 splice_region, splice_polypyrimidine_tract, intron
NM_021134.4 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00008258
2
Clinical Significance
Conservation
PhyloP100: -0.649
Genes affected
MRPL23 (HGNC:10322): (mitochondrial ribosomal protein L23) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. The gene is biallelically expressed, despite its location within a region of imprinted genes on chromosome 11. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 11-1952119-G-A is Benign according to our data. Variant chr11-1952119-G-A is described in ClinVar as [Benign]. Clinvar id is 791542.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL23 | NM_021134.4 | c.141-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000397298.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL23 | ENST00000397298.8 | c.141-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_021134.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 8AN: 17540Hom.: 0 Cov.: 2 FAILED QC
GnomAD3 genomes
?
AF:
AC:
8
AN:
17540
Hom.:
Cov.:
2
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00289 AC: 727AN: 251328Hom.: 6 AF XY: 0.00295 AC XY: 401AN XY: 135892
GnomAD3 exomes
AF:
AC:
727
AN:
251328
Hom.:
AF XY:
AC XY:
401
AN XY:
135892
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000277 AC: 27AN: 97538Hom.: 0 Cov.: 0 AF XY: 0.000271 AC XY: 14AN XY: 51684
GnomAD4 exome
AF:
AC:
27
AN:
97538
Hom.:
Cov.:
0
AF XY:
AC XY:
14
AN XY:
51684
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000456 AC: 8AN: 17554Hom.: 0 Cov.: 2 AF XY: 0.000258 AC XY: 2AN XY: 7746
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
8
AN:
17554
Hom.:
Cov.:
2
AF XY:
AC XY:
2
AN XY:
7746
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
7
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 12, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at