13-27256681-TG-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000461690.5(RPL21):n.*371delG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 637,700 control chromosomes in the GnomAD database, including 2,133 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.096 ( 898 hom., cov: 31)
Exomes 𝑓: 0.067 ( 1235 hom. )
Consequence
RPL21
ENST00000461690.5 non_coding_transcript_exon
ENST00000461690.5 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.36
Publications
0 publications found
Genes affected
RPL21 (HGNC:10313): (ribosomal protein L21) 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 L21E 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. [provided by RefSeq, Jul 2008]
RPL21 Gene-Disease associations (from GenCC):
- hypotrichosis 12Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- hypotrichosis simplexInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 13-27256681-TG-T is Benign according to our data. Variant chr13-27256681-TG-T is described in CliVar as Benign. Clinvar id is 1227239.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0964 AC: 14662AN: 152172Hom.: 892 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
14662
AN:
152172
Hom.:
Cov.:
31
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:
GnomAD4 exome AF: 0.0666 AC: 32329AN: 485410Hom.: 1235 Cov.: 0 AF XY: 0.0643 AC XY: 16843AN XY: 262078 show subpopulations
GnomAD4 exome
AF:
AC:
32329
AN:
485410
Hom.:
Cov.:
0
AF XY:
AC XY:
16843
AN XY:
262078
show subpopulations
African (AFR)
AF:
AC:
2228
AN:
12810
American (AMR)
AF:
AC:
2735
AN:
22096
Ashkenazi Jewish (ASJ)
AF:
AC:
1395
AN:
16456
East Asian (EAS)
AF:
AC:
2007
AN:
30978
South Asian (SAS)
AF:
AC:
2483
AN:
51644
European-Finnish (FIN)
AF:
AC:
2402
AN:
30392
Middle Eastern (MID)
AF:
AC:
152
AN:
2114
European-Non Finnish (NFE)
AF:
AC:
16917
AN:
291514
Other (OTH)
AF:
AC:
2010
AN:
27406
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
1433
2867
4300
5734
7167
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
138
276
414
552
690
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0964 AC: 14685AN: 152290Hom.: 898 Cov.: 31 AF XY: 0.0963 AC XY: 7168AN XY: 74468 show subpopulations
GnomAD4 genome
AF:
AC:
14685
AN:
152290
Hom.:
Cov.:
31
AF XY:
AC XY:
7168
AN XY:
74468
show subpopulations
African (AFR)
AF:
AC:
7279
AN:
41534
American (AMR)
AF:
AC:
1665
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
305
AN:
3470
East Asian (EAS)
AF:
AC:
257
AN:
5190
South Asian (SAS)
AF:
AC:
203
AN:
4832
European-Finnish (FIN)
AF:
AC:
814
AN:
10612
Middle Eastern (MID)
AF:
AC:
22
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3921
AN:
68030
Other (OTH)
AF:
AC:
191
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
657
1314
1972
2629
3286
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
148
296
444
592
740
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
202
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 14, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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