rs4903
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_003380.5(VIM):c.813C>T(p.Asp271Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00974 in 1,614,042 control chromosomes in the GnomAD database, including 1,147 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.049 ( 576 hom., cov: 33)
Exomes 𝑓: 0.0057 ( 571 hom. )
Consequence
VIM
NM_003380.5 synonymous
NM_003380.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
Genes affected
VIM (HGNC:12692): (vimentin) This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 10-17233862-C-T is Benign according to our data. Variant chr10-17233862-C-T is described in ClinVar as [Benign]. Clinvar id is 474044.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.28 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VIM | NM_003380.5 | c.813C>T | p.Asp271Asp | synonymous_variant | 5/10 | ENST00000544301.7 | NP_003371.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VIM | ENST00000544301.7 | c.813C>T | p.Asp271Asp | synonymous_variant | 5/10 | 1 | NM_003380.5 | ENSP00000446007.1 |
Frequencies
GnomAD3 genomes AF: 0.0488 AC: 7419AN: 152048Hom.: 576 Cov.: 33
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GnomAD3 exomes AF: 0.0139 AC: 3484AN: 251408Hom.: 229 AF XY: 0.0104 AC XY: 1417AN XY: 135882
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GnomAD4 exome AF: 0.00567 AC: 8293AN: 1461876Hom.: 571 Cov.: 31 AF XY: 0.00510 AC XY: 3711AN XY: 727236
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GnomAD4 genome AF: 0.0488 AC: 7428AN: 152166Hom.: 576 Cov.: 33 AF XY: 0.0474 AC XY: 3527AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 31, 2018 | 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. - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Cataract 30 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 20, 2024 | - - |
Computational scores
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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