5-120519026-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001300783.2(PRR16):c.159+54381C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,696 control chromosomes in the GnomAD database, including 6,793 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 0.28 ( 6793 hom., cov: 31)
Consequence
PRR16
NM_001300783.2 intron
NM_001300783.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.75
Publications
3 publications found
Genes affected
Genome browser will be placed here
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRR16 | ENST00000407149.7 | c.159+54381C>A | intron_variant | Intron 1 of 1 | 1 | NM_001300783.2 | ENSP00000385118.2 | |||
PRR16 | ENST00000379551.2 | c.90+37733C>A | intron_variant | Intron 2 of 2 | 1 | ENSP00000368869.2 | ||||
PRR16 | ENST00000509923.1 | c.-52+53315C>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000421256.1 |
Frequencies
GnomAD3 genomes AF: 0.282 AC: 42676AN: 151578Hom.: 6757 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
42676
AN:
151578
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.282 AC: 42758AN: 151696Hom.: 6793 Cov.: 31 AF XY: 0.277 AC XY: 20496AN XY: 74126 show subpopulations
GnomAD4 genome
AF:
AC:
42758
AN:
151696
Hom.:
Cov.:
31
AF XY:
AC XY:
20496
AN XY:
74126
show subpopulations
African (AFR)
AF:
AC:
17918
AN:
41282
American (AMR)
AF:
AC:
3294
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
AC:
850
AN:
3462
East Asian (EAS)
AF:
AC:
223
AN:
5176
South Asian (SAS)
AF:
AC:
877
AN:
4802
European-Finnish (FIN)
AF:
AC:
2233
AN:
10528
Middle Eastern (MID)
AF:
AC:
98
AN:
292
European-Non Finnish (NFE)
AF:
AC:
16576
AN:
67884
Other (OTH)
AF:
AC:
591
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1487
2975
4462
5950
7437
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
422
844
1266
1688
2110
<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:
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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