9-35684825-CG-CGG
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_003289.4(TPM2):c.564-19dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 1,596,748 control chromosomes in the GnomAD database, including 303,763 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 29446 hom., cov: 0)
Exomes 𝑓: 0.62 ( 274317 hom. )
Consequence
TPM2
NM_003289.4 intron
NM_003289.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.39
Genes affected
TPM2 (HGNC:12011): (tropomyosin 2) This gene encodes beta-tropomyosin, a member of the actin filament binding protein family, and mainly expressed in slow, type 1 muscle fibers. Mutations in this gene can alter the expression of other sarcomeric tropomyosin proteins, and cause cap disease, nemaline myopathy and distal arthrogryposis syndromes. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 9-35684825-C-CG is Benign according to our data. Variant chr9-35684825-C-CG is described in ClinVar as [Benign]. Clinvar id is 94123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPM2 | NM_003289.4 | c.564-19dupC | intron_variant | ENST00000645482.3 | NP_003280.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPM2 | ENST00000645482.3 | c.564-19dupC | intron_variant | NM_003289.4 | ENSP00000496494.2 |
Frequencies
GnomAD3 genomes AF: 0.624 AC: 93834AN: 150344Hom.: 29415 Cov.: 0
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GnomAD4 exome AF: 0.618 AC: 893752AN: 1446288Hom.: 274317 Cov.: 36 AF XY: 0.620 AC XY: 446208AN XY: 719346
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GnomAD4 genome AF: 0.624 AC: 93917AN: 150460Hom.: 29446 Cov.: 0 AF XY: 0.629 AC XY: 46210AN XY: 73418
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Eurofins Ntd Llc (ga) | Oct 18, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2016 | 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. - |
Arthrogryposis, distal, type 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at