4-39454955-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000661.5(RPL9):c.392-11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,609,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
RPL9
NM_000661.5 intron
NM_000661.5 intron
Scores
2
Splicing: ADA: 0.0002630
2
Clinical Significance
Conservation
PhyloP100: 1.15
Publications
0 publications found
Genes affected
RPL9 (HGNC:10369): (ribosomal protein L9) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L6P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 4-39454955-A-G is Benign according to our data. Variant chr4-39454955-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3627899.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 30 AD gene.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| RPL9 | ENST00000295955.14 | c.392-11T>C | intron_variant | Intron 5 of 7 | 1 | NM_000661.5 | ENSP00000346022.7 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
152164
Hom.:
Cov.:
33
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:
GnomAD2 exomes AF: 0.000118 AC: 29AN: 246718 AF XY: 0.000105 show subpopulations
GnomAD2 exomes
AF:
AC:
29
AN:
246718
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1457268Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 725018 show subpopulations
GnomAD4 exome
AF:
AC:
30
AN:
1457268
Hom.:
Cov.:
30
AF XY:
AC XY:
15
AN XY:
725018
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33328
American (AMR)
AF:
AC:
0
AN:
44186
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26066
East Asian (EAS)
AF:
AC:
27
AN:
39668
South Asian (SAS)
AF:
AC:
1
AN:
85430
European-Finnish (FIN)
AF:
AC:
0
AN:
53404
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1109154
Other (OTH)
AF:
AC:
2
AN:
60276
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.473
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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10
<30
30-35
35-40
40-45
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65-70
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>80
Age
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74476 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
152282
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
74476
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41552
American (AMR)
AF:
AC:
0
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
4
AN:
5184
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68024
Other (OTH)
AF:
AC:
0
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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4
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10
<30
30-35
35-40
40-45
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60-65
65-70
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 25, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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