rs778284038
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001018116.2(CAVIN4):c.939G>A(p.Glu313=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,612,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
CAVIN4
NM_001018116.2 synonymous
NM_001018116.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.44
Genes affected
CAVIN4 (HGNC:33742): (caveolae associated protein 4) This gene encodes a protein containing two coiled-coil regions. The encoded protein promotes Rho/ROCK (Rho-kinase) signaling in cardiac muscles cells, and may facilitate myofibrillar organization. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 9-100586295-G-A is Benign according to our data. Variant chr9-100586295-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 227561.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=2.44 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAVIN4 | NM_001018116.2 | c.939G>A | p.Glu313= | synonymous_variant | 2/2 | ENST00000307584.6 | |
CAVIN4 | XM_047423346.1 | c.915G>A | p.Glu305= | synonymous_variant | 3/3 | ||
CAVIN4 | XM_047423347.1 | c.552G>A | p.Glu184= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAVIN4 | ENST00000307584.6 | c.939G>A | p.Glu313= | synonymous_variant | 2/2 | 1 | NM_001018116.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250460Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135310
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GnomAD4 exome AF: 0.000120 AC: 175AN: 1460678Hom.: 0 Cov.: 33 AF XY: 0.000127 AC XY: 92AN XY: 726468
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74296
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 03, 2015 | p.Glu313Glu in exon 2 of MURC: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 5/66064 of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitu te.org). - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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