chr10-17229521-G-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003380.5(VIM):c.99G>T(p.Thr33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,608,148 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 3 hom. )
Consequence
VIM
NM_003380.5 synonymous
NM_003380.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.508
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 10-17229521-G-T is Benign according to our data. Variant chr10-17229521-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 703473.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.508 with no splicing effect.
BS2
?
High AC in GnomAd at 17 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIM | NM_003380.5 | c.99G>T | p.Thr33= | synonymous_variant | 2/10 | ENST00000544301.7 | |
VIM-AS1 | NR_108061.1 | n.465C>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIM | ENST00000544301.7 | c.99G>T | p.Thr33= | synonymous_variant | 2/10 | 1 | NM_003380.5 | P1 | |
VIM-AS1 | ENST00000605833.2 | n.498C>A | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152080Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000405 AC: 93AN: 229904Hom.: 2 AF XY: 0.000528 AC XY: 67AN XY: 126920
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GnomAD4 exome AF: 0.000201 AC: 292AN: 1455950Hom.: 3 Cov.: 32 AF XY: 0.000287 AC XY: 208AN XY: 724362
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
VIM-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cataract 30 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 11, 2020 | - - |
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