3-8745503-G-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_033337.3(CAV3):c.115-23G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 1,594,502 control chromosomes in the GnomAD database, including 5,703 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.091 ( 750 hom., cov: 32)
Exomes 𝑓: 0.079 ( 4953 hom. )
Consequence
CAV3
NM_033337.3 intron
NM_033337.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.08
Genes affected
CAV3 (HGNC:1529): (caveolin 3) This gene encodes a caveolin family member, which functions as a component of the caveolae plasma membranes found in most cell types. Caveolin proteins are proposed to be scaffolding proteins for organizing and concentrating certain caveolin-interacting molecules. Mutations identified in this gene lead to interference with protein oligomerization or intra-cellular routing, disrupting caveolae formation and resulting in Limb-Girdle muscular dystrophy type-1C (LGMD-1C), hyperCKemia or rippling muscle disease (RMD). Alternative splicing has been identified for this locus, with inclusion or exclusion of a differentially spliced intron. In addition, transcripts utilize multiple polyA sites and contain two potential translation initiation sites. [provided by RefSeq, Jul 2008]
OXTR (HGNC:8529): (oxytocin receptor) The protein encoded by this gene belongs to the G-protein coupled receptor family and acts as a receptor for oxytocin. Its activity is mediated by G proteins which activate a phosphatidylinositol-calcium second messenger system. The oxytocin-oxytocin receptor system plays an important role in the uterus during parturition. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 3-8745503-G-C is Benign according to our data. Variant chr3-8745503-G-C is described in ClinVar as [Benign]. Clinvar id is 31737.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-8745503-G-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAV3 | NM_033337.3 | c.115-23G>C | intron_variant | Intron 1 of 1 | ENST00000343849.3 | NP_203123.1 | ||
CAV3 | NM_001234.5 | c.115-23G>C | intron_variant | Intron 1 of 2 | NP_001225.1 | |||
OXTR | XR_007095681.1 | n.1885-2901C>G | intron_variant | Intron 4 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAV3 | ENST00000343849.3 | c.115-23G>C | intron_variant | Intron 1 of 1 | 1 | NM_033337.3 | ENSP00000341940.2 | |||
CAV3 | ENST00000397368.2 | c.115-23G>C | intron_variant | Intron 1 of 2 | 1 | ENSP00000380525.2 | ||||
CAV3 | ENST00000472766.1 | n.155+11513G>C | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0913 AC: 13886AN: 152018Hom.: 745 Cov.: 32
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GnomAD3 exomes AF: 0.0695 AC: 17134AN: 246556Hom.: 744 AF XY: 0.0683 AC XY: 9097AN XY: 133284
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GnomAD4 exome AF: 0.0791 AC: 114090AN: 1442366Hom.: 4953 Cov.: 29 AF XY: 0.0775 AC XY: 55731AN XY: 718650
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GnomAD4 genome AF: 0.0914 AC: 13910AN: 152136Hom.: 750 Cov.: 32 AF XY: 0.0920 AC XY: 6843AN XY: 74370
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ClinVar
Significance: Benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1Other:1
Apr 15, 2012
Leiden Muscular Dystrophy (CAV3)
Significance: not provided
Review Status: no classification provided
Collection Method: curation
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
not specified Benign:1
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PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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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