17-42998966-T-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000988.5(RPL27):c.81+135T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RPL27
NM_000988.5 intron
NM_000988.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.898
Publications
2 publications found
Genes affected
RPL27 (HGNC:10328): (ribosomal protein L27) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L27e family of ribosomal proteins and a component of the 60S subunit. A splice site mutation in this gene has been identified in a Diamond-Blackfan anemia (DBA) patient. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Mar 2017]
RPL27 Gene-Disease associations (from GenCC):
- Diamond-Blackfan anemia 16Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000988.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 152110Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
0
AN:
152110
Hom.:
Cov.:
30
Gnomad AFR
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Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 513964Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 274144
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
513964
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
274144
African (AFR)
AF:
AC:
0
AN:
13894
American (AMR)
AF:
AC:
0
AN:
23296
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
14524
East Asian (EAS)
AF:
AC:
0
AN:
31716
South Asian (SAS)
AF:
AC:
0
AN:
53014
European-Finnish (FIN)
AF:
AC:
0
AN:
33558
Middle Eastern (MID)
AF:
AC:
0
AN:
3688
European-Non Finnish (NFE)
AF:
AC:
0
AN:
312174
Other (OTH)
AF:
AC:
0
AN:
28100
GnomAD4 genome 0.00 AC: 0AN: 152110Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74296
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152110
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
74296
African (AFR)
AF:
AC:
0
AN:
41378
American (AMR)
AF:
AC:
0
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68040
Other (OTH)
AF:
AC:
0
AN:
2094
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
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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