rs3729761
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005184.4(CALM3):c.183C>T(p.Asn61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000767 in 1,613,490 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00041 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00080 ( 1 hom. )
Consequence
CALM3
NM_005184.4 synonymous
NM_005184.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
Genes affected
CALM3 (HGNC:1449): (calmodulin 3) This gene encodes a member of a family of proteins that binds calcium and functions as a enzymatic co-factor. Activity of this protein is important in the regulation of the cell cycle and cytokinesis. Multiple alternatively spliced transcript variants have been observed at this gene. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 19-46608486-C-T is Benign according to our data. Variant chr19-46608486-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 240116.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-46608486-C-T is described in Lovd as [Benign]. Variant chr19-46608486-C-T is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-1.28 with no splicing effect.
BS2
?
High AC in GnomAd4 at 63 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALM3 | NM_005184.4 | c.183C>T | p.Asn61= | synonymous_variant | 4/6 | ENST00000291295.14 | |
LOC124904729 | XR_007067276.1 | n.583G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALM3 | ENST00000291295.14 | c.183C>T | p.Asn61= | synonymous_variant | 4/6 | 1 | NM_005184.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000414 AC: 63AN: 152172Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000537 AC: 135AN: 251462Hom.: 0 AF XY: 0.000574 AC XY: 78AN XY: 135904
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GnomAD4 exome AF: 0.000803 AC: 1174AN: 1461200Hom.: 1 Cov.: 31 AF XY: 0.000795 AC XY: 578AN XY: 726936
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GnomAD4 genome ? AF: 0.000414 AC: 63AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74454
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ClinVar
Significance: Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 30, 2020 | This variant is associated with the following publications: (PMID: 26350513) - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jun 28, 2023 | - - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Long QT syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 28, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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