rs113699058
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001036.6(RYR3):c.6134+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,613,792 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 8 hom., cov: 31)
Exomes 𝑓: 0.00091 ( 16 hom. )
Consequence
RYR3
NM_001036.6 intron
NM_001036.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.527
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 15-33696500-T-C is Benign according to our data. Variant chr15-33696500-T-C is described in ClinVar as [Benign]. Clinvar id is 461934.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00643 (980/152308) while in subpopulation AFR AF= 0.022 (916/41578). AF 95% confidence interval is 0.0208. There are 8 homozygotes in gnomad4. There are 464 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR3 | NM_001036.6 | c.6134+9T>C | intron_variant | ENST00000634891.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.6134+9T>C | intron_variant | 1 | NM_001036.6 | P4 | |||
RYR3 | ENST00000389232.9 | c.6134+9T>C | intron_variant | 5 | A1 | ||||
RYR3 | ENST00000415757.7 | c.6134+9T>C | intron_variant | 2 | A2 | ||||
RYR3 | ENST00000634418.1 | c.6134+9T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00636 AC: 968AN: 152190Hom.: 7 Cov.: 31
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GnomAD3 exomes AF: 0.00199 AC: 492AN: 247676Hom.: 3 AF XY: 0.00167 AC XY: 224AN XY: 134386
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GnomAD4 exome AF: 0.000907 AC: 1326AN: 1461484Hom.: 16 Cov.: 32 AF XY: 0.000768 AC XY: 558AN XY: 727012
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GnomAD4 genome ? AF: 0.00643 AC: 980AN: 152308Hom.: 8 Cov.: 31 AF XY: 0.00623 AC XY: 464AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at