rs150120464
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_014000.3(VCL):c.1557C>A(p.Ile519Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000815 in 1,614,016 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014000.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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VCL | NM_014000.3 | c.1557C>A | p.Ile519Ile | synonymous_variant | Exon 12 of 22 | ENST00000211998.10 | NP_054706.1 | |
VCL | NM_003373.4 | c.1557C>A | p.Ile519Ile | synonymous_variant | Exon 12 of 21 | NP_003364.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00432 AC: 657AN: 152202Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00123 AC: 309AN: 251456Hom.: 3 AF XY: 0.000861 AC XY: 117AN XY: 135908
GnomAD4 exome AF: 0.000452 AC: 660AN: 1461696Hom.: 4 Cov.: 31 AF XY: 0.000384 AC XY: 279AN XY: 727144
GnomAD4 genome AF: 0.00431 AC: 656AN: 152320Hom.: 6 Cov.: 32 AF XY: 0.00431 AC XY: 321AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:6
Ile519Ile in Exon 12 of VCL: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue, is not located within t he splice consensus sequence and has been identified in 1.3% (49/3738) of Africa n American chromosomes from a broad population by the NHLBI Exome Sequencing Pro ject (http://evs.gs.washington.edu/EVS; dbSNP rs150120464). -
Variant summary: VCL c.1557C>A alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0022 in 277816 control chromosomes in the gnomAD database and literature, including 4 homozygotes. The observed variant frequency is approximately 87.11 fold of the estimated maximal expected allele frequency for a pathogenic variant in VCL causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is benign. c.1557C>A has been reported in the literature in one individual affected with palpitations (Campuzano_2012). This report does not provide unequivocal conclusions about association of the variant with Cardiomyopathy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. -
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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. -
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Cardiomyopathy Benign:1
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Dilated cardiomyopathy 1W Benign:1
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Dilated cardiomyopathy 1W;C2750459:Hypertrophic cardiomyopathy 15 Benign:1
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not provided Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at