NM_014976.2:c.1519-69T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014976.2(PDCD11):c.1519-69T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,554,042 control chromosomes in the GnomAD database, including 96,533 homozygotes. 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 0.31 ( 7541 hom., cov: 32)
Exomes 𝑓: 0.35 ( 88992 hom. )
Consequence
PDCD11
NM_014976.2 intron
NM_014976.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.02
Publications
24 publications found
Genes affected
PDCD11 (HGNC:13408): (programmed cell death 11) PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[supplied by OMIM, Oct 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDCD11 | ENST00000369797.8 | c.1519-69T>C | intron_variant | Intron 12 of 35 | 1 | NM_014976.2 | ENSP00000358812.3 | |||
PDCD11 | ENST00000649849.1 | c.1519-69T>C | intron_variant | Intron 12 of 35 | ENSP00000498205.1 |
Frequencies
GnomAD3 genomes AF: 0.309 AC: 46857AN: 151856Hom.: 7530 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
46857
AN:
151856
Hom.:
Cov.:
32
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: 0.353 AC: 494948AN: 1402068Hom.: 88992 AF XY: 0.350 AC XY: 242861AN XY: 693560 show subpopulations
GnomAD4 exome
AF:
AC:
494948
AN:
1402068
Hom.:
AF XY:
AC XY:
242861
AN XY:
693560
show subpopulations
African (AFR)
AF:
AC:
6652
AN:
32286
American (AMR)
AF:
AC:
18884
AN:
42204
Ashkenazi Jewish (ASJ)
AF:
AC:
8152
AN:
23516
East Asian (EAS)
AF:
AC:
17896
AN:
39166
South Asian (SAS)
AF:
AC:
22766
AN:
79300
European-Finnish (FIN)
AF:
AC:
16899
AN:
51772
Middle Eastern (MID)
AF:
AC:
1756
AN:
5540
European-Non Finnish (NFE)
AF:
AC:
381979
AN:
1070230
Other (OTH)
AF:
AC:
19964
AN:
58054
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
16328
32656
48985
65313
81641
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
12510
25020
37530
50040
62550
<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: 0.309 AC: 46897AN: 151974Hom.: 7541 Cov.: 32 AF XY: 0.309 AC XY: 22960AN XY: 74296 show subpopulations
GnomAD4 genome
AF:
AC:
46897
AN:
151974
Hom.:
Cov.:
32
AF XY:
AC XY:
22960
AN XY:
74296
show subpopulations
African (AFR)
AF:
AC:
8694
AN:
41462
American (AMR)
AF:
AC:
5789
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
1207
AN:
3466
East Asian (EAS)
AF:
AC:
2233
AN:
5160
South Asian (SAS)
AF:
AC:
1380
AN:
4810
European-Finnish (FIN)
AF:
AC:
3289
AN:
10582
Middle Eastern (MID)
AF:
AC:
86
AN:
294
European-Non Finnish (NFE)
AF:
AC:
23251
AN:
67918
Other (OTH)
AF:
AC:
677
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1653
3306
4959
6612
8265
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
476
952
1428
1904
2380
<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:
1290
AN:
3478
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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