NM_001018116.2:c.920G>C
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001018116.2(CAVIN4):c.920G>C(p.Ser307Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000795 in 1,597,514 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001018116.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAVIN4 | NM_001018116.2 | c.920G>C | p.Ser307Thr | missense_variant | Exon 2 of 2 | ENST00000307584.6 | NP_001018126.1 | |
CAVIN4 | XM_047423346.1 | c.896G>C | p.Ser299Thr | missense_variant | Exon 3 of 3 | XP_047279302.1 | ||
CAVIN4 | XM_047423347.1 | c.533G>C | p.Ser178Thr | missense_variant | Exon 2 of 2 | XP_047279303.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152134Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000992 AC: 24AN: 242044 AF XY: 0.000122 show subpopulations
GnomAD4 exome AF: 0.0000830 AC: 120AN: 1445380Hom.: 2 Cov.: 33 AF XY: 0.0000976 AC XY: 70AN XY: 716860 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74316 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Ser307Thr variant in MURC was identified in 1 Caucasian individual with DC M and segregated with disease in 2 affected family members (Rodriguez 2011). In vitro functional studies provide some evidence that the p.Ser307Thr variant may impact protein function (Rodriguez 2011). However, these types of assays may not accurately represent biological function. This variant has been identified in 6/13026 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http: //exac.broadinstitute.org). Computational prediction tools and conservation anal ysis suggest that the p.Ser307Thr variant may not impact the protein, though thi s information is not predictive enough to rule out pathogenicity. In summary, t he clinical significance of the p.Ser307Thr variant is uncertain. -
not provided Benign:1
This variant is associated with the following publications: (PMID: 21642240) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at