chr15-33680306-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001036.6(RYR3):c.5860+9750G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,172 control chromosomes in the GnomAD database, including 53,480 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 0.83 ( 53480 hom., cov: 33)
Consequence
RYR3
NM_001036.6 intron
NM_001036.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.288
Publications
4 publications found
Genes affected
RYR3 (HGNC:10485): (ryanodine receptor 3) The protein encoded by this gene is a ryanodine receptor, which functions to release calcium from intracellular storage for use in many cellular processes. For example, the encoded protein is involved in skeletal muscle contraction by releasing calcium from the sarcoplasmic reticulum followed by depolarization of T-tubules. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
RYR3 Gene-Disease associations (from GenCC):
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: LIMITED Submitted by: ClinGen, G2P
- congenital myopathyInheritance: AR Classification: NO_KNOWN Submitted by: ClinGen
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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 (AMR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.5860+9750G>A | intron_variant | Intron 38 of 103 | 1 | NM_001036.6 | ENSP00000489262.1 | |||
RYR3 | ENST00000389232.9 | c.5860+9750G>A | intron_variant | Intron 38 of 103 | 5 | ENSP00000373884.5 | ||||
RYR3 | ENST00000415757.7 | c.5860+9750G>A | intron_variant | Intron 38 of 102 | 2 | ENSP00000399610.3 | ||||
RYR3 | ENST00000634418.1 | c.5860+9750G>A | intron_variant | Intron 38 of 101 | 5 | ENSP00000489529.1 |
Frequencies
GnomAD3 genomes AF: 0.835 AC: 126933AN: 152054Hom.: 53429 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
126933
AN:
152054
Hom.:
Cov.:
33
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: 0.835 AC: 127039AN: 152172Hom.: 53480 Cov.: 33 AF XY: 0.836 AC XY: 62208AN XY: 74412 show subpopulations
GnomAD4 genome
AF:
AC:
127039
AN:
152172
Hom.:
Cov.:
33
AF XY:
AC XY:
62208
AN XY:
74412
show subpopulations
African (AFR)
AF:
AC:
29448
AN:
41456
American (AMR)
AF:
AC:
13834
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
2963
AN:
3472
East Asian (EAS)
AF:
AC:
4634
AN:
5172
South Asian (SAS)
AF:
AC:
3974
AN:
4826
European-Finnish (FIN)
AF:
AC:
9143
AN:
10604
Middle Eastern (MID)
AF:
AC:
251
AN:
294
European-Non Finnish (NFE)
AF:
AC:
60172
AN:
68022
Other (OTH)
AF:
AC:
1776
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1078
2157
3235
4314
5392
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
884
1768
2652
3536
4420
<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:
2914
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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