X-101391786-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP6_Very_StrongBP7BS2
The NM_021029.6(RPL36A):c.141C>T(p.Gly47Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00635 in 1,208,700 control chromosomes in the GnomAD database, including 18 homozygotes. There are 2,493 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0042 ( 2 hom., 141 hem., cov: 22)
Exomes 𝑓: 0.0066 ( 16 hom. 2352 hem. )
Consequence
RPL36A
NM_021029.6 synonymous
NM_021029.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.06
Genes affected
RPL36A (HGNC:10359): (ribosomal protein L36a) Cytoplasmic ribosomes, 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, which shares sequence similarity with yeast ribosomal protein L44, belongs to the L44E (L36AE) family of ribosomal proteins. Although this gene has been referred to as ribosomal protein L44 (RPL44), its official name is ribosomal protein L36a (RPL36A). This gene and the human gene officially named ribosomal protein L36a-like (RPL36AL) encode nearly identical proteins; however, they are distinct genes. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Naturally occurring read-through transcription occurs between this locus and the heterogeneous nuclear ribonucleoprotein H2 (H') gene. [provided by RefSeq, Jan 2011]
RPL36A-HNRNPH2 (HGNC:48349): (RPL36A-HNRNPH2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring ribosomal protein L36a and heterogeneous nuclear ribonucleoprotein H2 (H') genes on chromosome X. The read-through transcript produces a protein with similarity to the protein encoded by the upstream locus, ribosomal protein L36a. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -13 ACMG points.
BP6
Variant X-101391786-C-T is Benign according to our data. Variant chrX-101391786-C-T is described in ClinVar as [Benign]. Clinvar id is 708163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-101391786-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-1.06 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL36A | NM_021029.6 | c.141C>T | p.Gly47Gly | synonymous_variant | Exon 3 of 5 | ENST00000553110.8 | NP_066357.3 | |
RPL36A-HNRNPH2 | NM_001199973.2 | c.141C>T | p.Gly47Gly | synonymous_variant | Exon 3 of 5 | NP_001186902.2 | ||
RPL36A-HNRNPH2 | NM_001199974.2 | c.141C>T | p.Gly47Gly | synonymous_variant | Exon 3 of 4 | NP_001186903.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPL36A | ENST00000553110.8 | c.141C>T | p.Gly47Gly | synonymous_variant | Exon 3 of 5 | 1 | NM_021029.6 | ENSP00000446503.2 | ||
RPL36A-HNRNPH2 | ENST00000409170.3 | c.141C>T | p.Gly47Gly | synonymous_variant | Exon 3 of 5 | 4 | ENSP00000386655.4 |
Frequencies
GnomAD3 genomes AF: 0.00421 AC: 470AN: 111760Hom.: 2 Cov.: 22 show subpopulations
GnomAD3 genomes
AF:
AC:
470
AN:
111760
Hom.:
Cov.:
22
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GnomAD2 exomes AF: 0.00407 AC: 738AN: 181291 AF XY: 0.00393 show subpopulations
GnomAD2 exomes
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AC:
738
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181291
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GnomAD4 exome AF: 0.00657 AC: 7204AN: 1096883Hom.: 16 Cov.: 31 AF XY: 0.00649 AC XY: 2352AN XY: 362297 show subpopulations
GnomAD4 exome
AF:
AC:
7204
AN:
1096883
Hom.:
Cov.:
31
AF XY:
AC XY:
2352
AN XY:
362297
Gnomad4 AFR exome
AF:
AC:
17
AN:
26324
Gnomad4 AMR exome
AF:
AC:
45
AN:
34870
Gnomad4 ASJ exome
AF:
AC:
37
AN:
19309
Gnomad4 EAS exome
AF:
AC:
0
AN:
30199
Gnomad4 SAS exome
AF:
AC:
108
AN:
53682
Gnomad4 FIN exome
AF:
AC:
156
AN:
40519
Gnomad4 NFE exome
AF:
AC:
6591
AN:
841800
Gnomad4 Remaining exome
AF:
AC:
243
AN:
46055
Heterozygous variant carriers
0
308
617
925
1234
1542
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
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252
504
756
1008
1260
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Age
GnomAD4 genome AF: 0.00420 AC: 470AN: 111817Hom.: 2 Cov.: 22 AF XY: 0.00415 AC XY: 141AN XY: 33983 show subpopulations
GnomAD4 genome
AF:
AC:
470
AN:
111817
Hom.:
Cov.:
22
AF XY:
AC XY:
141
AN XY:
33983
Gnomad4 AFR
AF:
AC:
0.000876766
AN:
0.000876766
Gnomad4 AMR
AF:
AC:
0.00515021
AN:
0.00515021
Gnomad4 ASJ
AF:
AC:
0.00188466
AN:
0.00188466
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.001114
AN:
0.001114
Gnomad4 FIN
AF:
AC:
0.00282533
AN:
0.00282533
Gnomad4 NFE
AF:
AC:
0.00674939
AN:
0.00674939
Gnomad4 OTH
AF:
AC:
0.00327225
AN:
0.00327225
Heterozygous variant carriers
0
17
34
50
67
84
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
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Age
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Mar 29, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=298/2
polymorphism (auto)
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